Faizul Azam
May 15, 2023, 2:09:48 PM5/15/23
to gmx_MMPBSA
Hi!!
Please help me fixing the following error:
Thanks!!
(base) conda activate gmxMMPBSA
WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or
- Make your system-wide implementation visible by installing ocl-icd-system conda package.
(gmxMMPBSA) mpirun -np 8 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
tets
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[ERROR ] MMPBSA_Error
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[ERROR ] MMPBSA_Error
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 870, in get_cl_args
self.FILES = self.clparser.parse_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1825, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1858, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2067, in _parse_known_args
start_index = consume_optional(start_index)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2007, in consume_optional
take_action(action, args, option_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1919, in take_action
argument_values = self._get_values(action, argument_strings)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2450, in _get_values
value = self._get_value(action, arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2483, in _get_value
result = type_func(arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/commandlineparser.py", line 60, in gmx_MMPBSA_file
GMXMMPBSA_ERROR(f'{result} do not exist or is inaccessible')
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[ERROR ] MMPBSA_Error
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[ERROR ] MMPBSA_Error
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 870, in get_cl_args
self.FILES = self.clparser.parse_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1825, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1858, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2067, in _parse_known_args
start_index = consume_optional(start_index)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2007, in consume_optional
take_action(action, args, option_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1919, in take_action
argument_values = self._get_values(action, argument_strings)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2450, in _get_values
value = self._get_value(action, arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2483, in _get_value
result = type_func(arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/commandlineparser.py", line 60, in gmx_MMPBSA_file
GMXMMPBSA_ERROR(f'{result} do not exist or is inaccessible')
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
tets
tets
tets
[ERROR ] MMPBSA_Error
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 870, in get_cl_args
self.FILES = self.clparser.parse_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1825, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1858, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2067, in _parse_known_args
start_index = consume_optional(start_index)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2007, in consume_optional
take_action(action, args, option_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1919, in take_action
argument_values = self._get_values(action, argument_strings)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2450, in _get_values
value = self._get_value(action, arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2483, in _get_value
result = type_func(arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/commandlineparser.py", line 60, in gmx_MMPBSA_file
GMXMMPBSA_ERROR(f'{result} do not exist or is inaccessible')
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
tets
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 870, in get_cl_args
self.FILES = self.clparser.parse_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1825, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1858, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2067, in _parse_known_args
start_index = consume_optional(start_index)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2007, in consume_optional
take_action(action, args, option_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1919, in take_action
argument_values = self._get_values(action, argument_strings)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2450, in _get_values
value = self._get_value(action, arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2483, in _get_value
result = type_func(arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/commandlineparser.py", line 60, in gmx_MMPBSA_file
GMXMMPBSA_ERROR(f'{result} do not exist or is inaccessible')
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 870, in get_cl_args
self.FILES = self.clparser.parse_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1825, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1858, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2067, in _parse_known_args
start_index = consume_optional(start_index)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2007, in consume_optional
take_action(action, args, option_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1919, in take_action
argument_values = self._get_values(action, argument_strings)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2450, in _get_values
value = self._get_value(action, arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2483, in _get_value
result = type_func(arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/commandlineparser.py", line 60, in gmx_MMPBSA_file
GMXMMPBSA_ERROR(f'{result} do not exist or is inaccessible')
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[ERROR ] MMPBSA_Error
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
tets
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 870, in get_cl_args
self.FILES = self.clparser.parse_args(args)
[INFO ] Starting gmx_MMPBSA v1.6.1
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1825, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1858, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2067, in _parse_known_args
start_index = consume_optional(start_index)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2007, in consume_optional
take_action(action, args, option_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1919, in take_action
argument_values = self._get_values(action, argument_strings)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2450, in _get_values
value = self._get_value(action, arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2483, in _get_value
result = type_func(arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/commandlineparser.py", line 60, in gmx_MMPBSA_file
GMXMMPBSA_ERROR(f'{result} do not exist or is inaccessible')
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
tets
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[ERROR ] MMPBSA_Error
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 870, in get_cl_args
self.FILES = self.clparser.parse_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1825, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1858, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2067, in _parse_known_args
start_index = consume_optional(start_index)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2007, in consume_optional
take_action(action, args, option_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1919, in take_action
argument_values = self._get_values(action, argument_strings)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2450, in _get_values
value = self._get_value(action, arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2483, in _get_value
result = type_func(arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/commandlineparser.py", line 60, in gmx_MMPBSA_file
GMXMMPBSA_ERROR(f'{result} do not exist or is inaccessible')
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
tets
[ERROR ] MMPBSA_Error
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 870, in get_cl_args
self.FILES = self.clparser.parse_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1825, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1858, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2067, in _parse_known_args
start_index = consume_optional(start_index)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2007, in consume_optional
take_action(action, args, option_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1919, in take_action
argument_values = self._get_values(action, argument_strings)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2450, in _get_values
value = self._get_value(action, arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2483, in _get_value
result = type_func(arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/commandlineparser.py", line 60, in gmx_MMPBSA_file
GMXMMPBSA_ERROR(f'{result} do not exist or is inaccessible')
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[37672,1],3]
Exit code: 1
--------------------------------------------------------------------------
(gmxMMPBSA) mpirun -np 8 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
tets
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
tets
tets
tets
tets
tets
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Checking external programs...
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] Checking mmpbsa.in input file...
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] Checking external programs...Done.
[INFO ] Checking external programs...
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
tets
tets
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[ERROR ] MMPBSA_Error
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 289, in gmx2pdb
GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(comprog), self.FILES.complex_trajs[0]))
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[ERROR ] MMPBSA_Error
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
[ERROR ] MMPBSA_Error
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
[ERROR ] MMPBSA_Error
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 289, in gmx2pdb
GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(comprog), self.FILES.complex_trajs[0]))
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 289, in gmx2pdb
GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(comprog), self.FILES.complex_trajs[0]))
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 289, in gmx2pdb
GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(comprog), self.FILES.complex_trajs[0]))
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Checking the structures consistency...
[WARNING] No reference structure was found and the complex structure not contain any chain ID. Assigning chains ID automatically...
[INFO ]
[INFO ] Using topology conversion. Setting radiopt = 0...
[INFO ] Building Normal Complex Amber topology...
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
tops = self.gmxtop2prmtop()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 534, in gmxtop2prmtop
com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 822, in cleantop
rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
self.read(fname, defines, parametrize)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 289, in read
for line in f:
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_gromacsfile.py", line 44, in __iter__
for line in self._handle:
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 175, in __iter__
self._ppcmdmap[cmd](self, args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 30, in wrapper
return func(self, args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 288, in _pp_include
raise PreProcessorError('Could not find %s' % includefile)
PreProcessorError: Could not find Ligand.itp
Exiting. All files have been retained.
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Checking the structures consistency...
[WARNING] No reference structure was found and the complex structure not contain any chain ID. Assigning chains ID automatically...
[INFO ]
[INFO ] Using topology conversion. Setting radiopt = 0...
[INFO ] Building Normal Complex Amber topology...
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
tops = self.gmxtop2prmtop()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 534, in gmxtop2prmtop
com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 822, in cleantop
rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
self.read(fname, defines, parametrize)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 289, in read
for line in f:
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_gromacsfile.py", line 44, in __iter__
for line in self._handle:
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 175, in __iter__
self._ppcmdmap[cmd](self, args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 30, in wrapper
return func(self, args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 288, in _pp_include
raise PreProcessorError('Could not find %s' % includefile)
PreProcessorError: Could not find Ligand.itp
Exiting. All files have been retained.
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 521, in _parse_atom_parts
parts = cls._parse_atom_parts_1(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 512, in _parse_atom_parts_1
number=line[6:11], name=line[12:16].strip(), alternate_location=line[16].strip(),
IndexError: string index out of range
Exiting. All files have been retained.
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Checking the structures consistency...
[WARNING] No reference structure was found and the complex structure not contain any chain ID. Assigning chains ID automatically...
[INFO ]
[INFO ] Using topology conversion. Setting radiopt = 0...
[INFO ] Building Normal Complex Amber topology...
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
tops = self.gmxtop2prmtop()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 534, in gmxtop2prmtop
com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 822, in cleantop
rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
self.read(fname, defines, parametrize)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 289, in read
for line in f:
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_gromacsfile.py", line 44, in __iter__
for line in self._handle:
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 175, in __iter__
self._ppcmdmap[cmd](self, args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 30, in wrapper
return func(self, args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 288, in _pp_include
raise PreProcessorError('Could not find %s' % includefile)
PreProcessorError: Could not find Ligand.itp
Exiting. All files have been retained.
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[37906,1],6]
Exit code: 1
--------------------------------------------------------------------------
(gmxMMPBSA) mpirun -np 8 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 674, in make_prmtops
self.remove(-1)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1154, in remove
utils.remove(flag, fnpre=self.pre)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 715, in remove
os.remove(fil)
FileNotFoundError: [Errno 2] No such file or directory: '#_GMXMMPBSA_COM_index.ndx.1#'
Exiting. All files have been retained.
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
tets
tets
tets
tets
tets
tets
tets
[INFO ] Checking external programs...
[INFO ] Checking mmpbsa.in input file...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking external programs...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Checking mmpbsa.in input file...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking external programs...
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] Checking external programs...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] Checking external programs...
[INFO ] Checking external programs...
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] Checking external programs...Done.
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Making gmx_MMPBSA index for complex...
tets
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[ERROR ] MMPBSA_Error
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 289, in gmx2pdb
GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(comprog), self.FILES.complex_trajs[0]))
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 521, in _parse_atom_parts
parts = cls._parse_atom_parts_1(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 512, in _parse_atom_parts_1
number=line[6:11], name=line[12:16].strip(), alternate_location=line[16].strip(),
IndexError: string index out of range
Exiting. All files have been retained.
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 484, in gmx2pdb
self.receptor_str = self.molstr(self.receptor_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 523, in _parse_atom_parts
x=float(line[30:38]), y=float(line[38:46]), z=float(line[46:54]),
ValueError: could not convert string to float: '\x00\x00\x00\x00\x00\x00\x00\x00'
Exiting. All files have been retained.
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 484, in gmx2pdb
self.receptor_str = self.molstr(self.receptor_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 523, in _parse_atom_parts
x=float(line[30:38]), y=float(line[38:46]), z=float(line[46:54]),
ValueError: could not convert string to float: '\x00\x00\x00\x00\x00\x00\x00\x00'
Exiting. All files have been retained.
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 484, in gmx2pdb
self.receptor_str = self.molstr(self.receptor_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 523, in _parse_atom_parts
x=float(line[30:38]), y=float(line[38:46]), z=float(line[46:54]),
ValueError: could not convert string to float: '\x00\x00\x00\x00\x00\x00\x00\x00'
Exiting. All files have been retained.
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 523, in _parse_atom_parts
x=float(line[30:38]), y=float(line[38:46]), z=float(line[46:54]),
ValueError: could not convert string to float: ''
Exiting. All files have been retained.
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 523, in _parse_atom_parts
x=float(line[30:38]), y=float(line[38:46]), z=float(line[46:54]),
ValueError: could not convert string to float: ''
Exiting. All files have been retained.
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[38207,1],6]
Exit code: 1
--------------------------------------------------------------------------
(gmxMMPBSA) mpirun -np 8 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
tets
[INFO ] Starting gmx_MMPBSA v1.6.1
tets
tets
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking mmpbsa.in input file...
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
tets
tets
tets
tets
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 674, in make_prmtops
self.remove(-1)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1154, in remove
utils.remove(flag, fnpre=self.pre)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 715, in remove
os.remove(fil)
FileNotFoundError: [Errno 2] No such file or directory: '#_GMXMMPBSA_COM_index.ndx.1#'
Exiting. All files have been retained.
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 674, in make_prmtops
self.remove(-1)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1154, in remove
utils.remove(flag, fnpre=self.pre)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 715, in remove
os.remove(fil)
FileNotFoundError: [Errno 2] No such file or directory: '#_GMXMMPBSA_COM_index.ndx.3#'
Exiting. All files have been retained.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Checking external programs...Done.
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Making gmx_MMPBSA index for complex...
tets
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[ERROR ] MMPBSA_Error
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 289, in gmx2pdb
GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(comprog), self.FILES.complex_trajs[0]))
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Checking the structures consistency...
[WARNING] No reference structure was found and the complex structure not contain any chain ID. Assigning chains ID automatically...
[INFO ]
[INFO ] Using topology conversion. Setting radiopt = 0...
[INFO ] Building Normal Complex Amber topology...
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
tops = self.gmxtop2prmtop()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 534, in gmxtop2prmtop
com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 822, in cleantop
rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
self.read(fname, defines, parametrize)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 461, in read
self.parametrize()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 1102, in parametrize
raise ParameterError('Not all improper torsion '
ParameterError: Not all improper torsion parameters found
Exiting. All files have been retained.
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Checking the structures consistency...
[WARNING] No reference structure was found and the complex structure not contain any chain ID. Assigning chains ID automatically...
[INFO ]
[INFO ] Using topology conversion. Setting radiopt = 0...
[INFO ] Building Normal Complex Amber topology...
[ERROR ] MMPBSA_Error
The atom 1537 in the complex index is not found in the topology file. Please check that the files are consistent.
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
tops = self.gmxtop2prmtop()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 534, in gmxtop2prmtop
com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 832, in cleantop
GMXMMPBSA_ERROR(f'The atom {i} in the {id} index is not found in the topology file. Please check that '
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
The atom 1537 in the complex index is not found in the topology file. Please check that the files are consistent.
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Checking the structures consistency...
[WARNING] No reference structure was found and the complex structure not contain any chain ID. Assigning chains ID automatically...
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 493, in gmx2pdb
self.check_structures(self.complex_str, self.receptor_str, self.ligand_str)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1305, in check_structures
self._assign_chains_IDs(com_str, rec_str, lig_str)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1333, in _assign_chains_IDs
rec_str.residues[i].chain = res.chain
IndexError: list index out of range
Exiting. All files have been retained.
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Checking the structures consistency...
[WARNING] No reference structure was found and the complex structure not contain any chain ID. Assigning chains ID automatically...
[INFO ]
[INFO ] Using topology conversion. Setting radiopt = 0...
[INFO ] Building Normal Complex Amber topology...
[ERROR ] MMPBSA_Error
The atom 299 in the complex index is not found in the topology file. Please check that the files are consistent.
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
tops = self.gmxtop2prmtop()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 534, in gmxtop2prmtop
com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 832, in cleantop
GMXMMPBSA_ERROR(f'The atom {i} in the {id} index is not found in the topology file. Please check that '
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
The atom 299 in the complex index is not found in the topology file. Please check that the files are consistent.
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 521, in _parse_atom_parts
parts = cls._parse_atom_parts_1(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 512, in _parse_atom_parts_1
number=line[6:11], name=line[12:16].strip(), alternate_location=line[16].strip(),
IndexError: string index out of range
Exiting. All files have been retained.
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[38887,1],3]
Exit code: 1
--------------------------------------------------------------------------
(gmxMMPBSA) mpirun -np 8 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
tets
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Making gmx_MMPBSA index for complex...
tets
tets
tets
tets
tets
tets
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Checking external programs...Done.
[INFO ] Checking mmpbsa.in input file...
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Making gmx_MMPBSA index for complex...
tets
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking mmpbsa.in input file...
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Checking external programs...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[ERROR ] MMPBSA_Error
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 487, in gmx2pdb
self.ref_str = check_str(self.FILES.reference_structure, ref=True)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 517, in check_str
GMXMMPBSA_ERROR('The reference structure used is inconsistent. The following residue does not have a '
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[ERROR ] MMPBSA_Error
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 487, in gmx2pdb
self.ref_str = check_str(self.FILES.reference_structure, ref=True)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 517, in check_str
GMXMMPBSA_ERROR('The reference structure used is inconsistent. The following residue does not have a '
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
[ERROR ] MMPBSA_Error
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 487, in gmx2pdb
self.ref_str = check_str(self.FILES.reference_structure, ref=True)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 517, in check_str
GMXMMPBSA_ERROR('The reference structure used is inconsistent. The following residue does not have a '
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[ERROR ] MMPBSA_Error
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 487, in gmx2pdb
self.ref_str = check_str(self.FILES.reference_structure, ref=True)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 517, in check_str
GMXMMPBSA_ERROR('The reference structure used is inconsistent. The following residue does not have a '
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[ERROR ] MMPBSA_Error
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 487, in gmx2pdb
self.ref_str = check_str(self.FILES.reference_structure, ref=True)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 517, in check_str
GMXMMPBSA_ERROR('The reference structure used is inconsistent. The following residue does not have a '
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[ERROR ] MMPBSA_Error
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 487, in gmx2pdb
self.ref_str = check_str(self.FILES.reference_structure, ref=True)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 517, in check_str
GMXMMPBSA_ERROR('The reference structure used is inconsistent. The following residue does not have a '
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[ERROR ] MMPBSA_Error
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 487, in gmx2pdb
self.ref_str = check_str(self.FILES.reference_structure, ref=True)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 517, in check_str
GMXMMPBSA_ERROR('The reference structure used is inconsistent. The following residue does not have a '
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[ERROR ] MMPBSA_Error
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 487, in gmx2pdb
self.ref_str = check_str(self.FILES.reference_structure, ref=True)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 517, in check_str
GMXMMPBSA_ERROR('The reference structure used is inconsistent. The following residue does not have a '
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[38948,1],4]
Exit code: 1
--------------------------------------------------------------------------
(gmxMMPBSA) mpirun -np 8 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
tets
tets
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[ERROR ] MMPBSA_Error
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 869, in get_cl_args
utils._get_dup_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 469, in _get_dup_args
GMXMMPBSA_ERROR('Several args are duplicated in the command-line...\n'
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Starting gmx_MMPBSA v1.6.1
[ERROR ] MMPBSA_Error
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 869, in get_cl_args
utils._get_dup_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 469, in _get_dup_args
GMXMMPBSA_ERROR('Several args are duplicated in the command-line...\n'
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
tets
[ERROR ] MMPBSA_Error
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
tets
tets
tets
tets
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 869, in get_cl_args
utils._get_dup_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 469, in _get_dup_args
GMXMMPBSA_ERROR('Several args are duplicated in the command-line...\n'
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[ERROR ] MMPBSA_Error
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 869, in get_cl_args
utils._get_dup_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 469, in _get_dup_args
GMXMMPBSA_ERROR('Several args are duplicated in the command-line...\n'
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[ERROR ] MMPBSA_Error
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[ERROR ] MMPBSA_Error
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 869, in get_cl_args
utils._get_dup_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 469, in _get_dup_args
GMXMMPBSA_ERROR('Several args are duplicated in the command-line...\n'
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[ERROR ] MMPBSA_Error
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 869, in get_cl_args
utils._get_dup_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 469, in _get_dup_args
GMXMMPBSA_ERROR('Several args are duplicated in the command-line...\n'
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 869, in get_cl_args
utils._get_dup_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 469, in _get_dup_args
GMXMMPBSA_ERROR('Several args are duplicated in the command-line...\n'
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
tets
[ERROR ] MMPBSA_Error
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 869, in get_cl_args
utils._get_dup_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 469, in _get_dup_args
GMXMMPBSA_ERROR('Several args are duplicated in the command-line...\n'
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[39207,1],2]
Exit code: 1
--------------------------------------------------------------------------
(gmxMMPBSA) mpirun -np 8 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
tets
tets
tets
tets
tets
tets
tets
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 674, in make_prmtops
self.remove(-1)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1154, in remove
utils.remove(flag, fnpre=self.pre)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 715, in remove
os.remove(fil)
FileNotFoundError: [Errno 2] No such file or directory: '#_GMXMMPBSA_REC.pdb.7#'
Exiting. All files have been retained.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 674, in make_prmtops
self.remove(-1)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1154, in remove
utils.remove(flag, fnpre=self.pre)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 715, in remove
os.remove(fil)
FileNotFoundError: [Errno 2] No such file or directory: '#_GMXMMPBSA_REC.pdb.7#'
Exiting. All files have been retained.
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
tets
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking mmpbsa.in input file...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] Checking mmpbsa.in input file...
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 523, in _parse_atom_parts
x=float(line[30:38]), y=float(line[38:46]), z=float(line[46:54]),
ValueError: could not convert string to float: '\x00\x00\x00\x00\x00\x00\x00\x00'
Exiting. All files have been retained.
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 383, in parse
inst.struct.assign_bonds()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/structure.py", line 976, in assign_bonds
pairs = find_atom_pairs(self, mindist, unassigned_atoms)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/utils/pairlist.py", line 39, in find_atom_pairs
voxels = np.array((coords - coords.min(axis=0)) / dist, dtype=int)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/numpy/core/_methods.py", line 45, in _amin
return umr_minimum(a, axis, None, out, keepdims, initial, where)
ValueError: zero-size array to reduction operation minimum which has no identity
Exiting. All files have been retained.
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 523, in _parse_atom_parts
x=float(line[30:38]), y=float(line[38:46]), z=float(line[46:54]),
ValueError: could not convert string to float: '\x00\x00\x00\x00\x00\x00\x00\x00'
Exiting. All files have been retained.
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 523, in _parse_atom_parts
x=float(line[30:38]), y=float(line[38:46]), z=float(line[46:54]),
ValueError: could not convert string to float: '\x00\x00\x00\x00\x00\x00\x00\x00'
Exiting. All files have been retained.
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 523, in _parse_atom_parts
x=float(line[30:38]), y=float(line[38:46]), z=float(line[46:54]),
ValueError: could not convert string to float: '\x00\x00\x00\x00\x00\x00\x00\x00'
Exiting. All files have been retained.
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 383, in parse
inst.struct.assign_bonds()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/structure.py", line 976, in assign_bonds
pairs = find_atom_pairs(self, mindist, unassigned_atoms)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/utils/pairlist.py", line 39, in find_atom_pairs
voxels = np.array((coords - coords.min(axis=0)) / dist, dtype=int)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/numpy/core/_methods.py", line 45, in _amin
return umr_minimum(a, axis, None, out, keepdims, initial, where)
ValueError: zero-size array to reduction operation minimum which has no identity
Exiting. All files have been retained.
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[39568,1],3]
Exit code: 1
--------------------------------------------------------------------------
(gmxMMPBSA)
WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or
- Make your system-wide implementation visible by installing ocl-icd-system conda package.
(gmxMMPBSA) mpirun -np 8 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
tets
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[ERROR ] MMPBSA_Error
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[ERROR ] MMPBSA_Error
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 870, in get_cl_args
self.FILES = self.clparser.parse_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1825, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1858, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2067, in _parse_known_args
start_index = consume_optional(start_index)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2007, in consume_optional
take_action(action, args, option_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1919, in take_action
argument_values = self._get_values(action, argument_strings)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2450, in _get_values
value = self._get_value(action, arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2483, in _get_value
result = type_func(arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/commandlineparser.py", line 60, in gmx_MMPBSA_file
GMXMMPBSA_ERROR(f'{result} do not exist or is inaccessible')
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[ERROR ] MMPBSA_Error
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[ERROR ] MMPBSA_Error
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 870, in get_cl_args
self.FILES = self.clparser.parse_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1825, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1858, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2067, in _parse_known_args
start_index = consume_optional(start_index)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2007, in consume_optional
take_action(action, args, option_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1919, in take_action
argument_values = self._get_values(action, argument_strings)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2450, in _get_values
value = self._get_value(action, arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2483, in _get_value
result = type_func(arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/commandlineparser.py", line 60, in gmx_MMPBSA_file
GMXMMPBSA_ERROR(f'{result} do not exist or is inaccessible')
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
tets
tets
tets
[ERROR ] MMPBSA_Error
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 870, in get_cl_args
self.FILES = self.clparser.parse_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1825, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1858, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2067, in _parse_known_args
start_index = consume_optional(start_index)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2007, in consume_optional
take_action(action, args, option_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1919, in take_action
argument_values = self._get_values(action, argument_strings)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2450, in _get_values
value = self._get_value(action, arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2483, in _get_value
result = type_func(arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/commandlineparser.py", line 60, in gmx_MMPBSA_file
GMXMMPBSA_ERROR(f'{result} do not exist or is inaccessible')
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
tets
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 870, in get_cl_args
self.FILES = self.clparser.parse_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1825, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1858, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2067, in _parse_known_args
start_index = consume_optional(start_index)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2007, in consume_optional
take_action(action, args, option_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1919, in take_action
argument_values = self._get_values(action, argument_strings)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2450, in _get_values
value = self._get_value(action, arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2483, in _get_value
result = type_func(arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/commandlineparser.py", line 60, in gmx_MMPBSA_file
GMXMMPBSA_ERROR(f'{result} do not exist or is inaccessible')
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 870, in get_cl_args
self.FILES = self.clparser.parse_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1825, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1858, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2067, in _parse_known_args
start_index = consume_optional(start_index)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2007, in consume_optional
take_action(action, args, option_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1919, in take_action
argument_values = self._get_values(action, argument_strings)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2450, in _get_values
value = self._get_value(action, arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2483, in _get_value
result = type_func(arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/commandlineparser.py", line 60, in gmx_MMPBSA_file
GMXMMPBSA_ERROR(f'{result} do not exist or is inaccessible')
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[ERROR ] MMPBSA_Error
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
tets
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 870, in get_cl_args
self.FILES = self.clparser.parse_args(args)
[INFO ] Starting gmx_MMPBSA v1.6.1
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1825, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1858, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2067, in _parse_known_args
start_index = consume_optional(start_index)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2007, in consume_optional
take_action(action, args, option_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1919, in take_action
argument_values = self._get_values(action, argument_strings)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2450, in _get_values
value = self._get_value(action, arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2483, in _get_value
result = type_func(arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/commandlineparser.py", line 60, in gmx_MMPBSA_file
GMXMMPBSA_ERROR(f'{result} do not exist or is inaccessible')
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
tets
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[ERROR ] MMPBSA_Error
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 870, in get_cl_args
self.FILES = self.clparser.parse_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1825, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1858, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2067, in _parse_known_args
start_index = consume_optional(start_index)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2007, in consume_optional
take_action(action, args, option_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1919, in take_action
argument_values = self._get_values(action, argument_strings)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2450, in _get_values
value = self._get_value(action, arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2483, in _get_value
result = type_func(arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/commandlineparser.py", line 60, in gmx_MMPBSA_file
GMXMMPBSA_ERROR(f'{result} do not exist or is inaccessible')
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
tets
[ERROR ] MMPBSA_Error
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 870, in get_cl_args
self.FILES = self.clparser.parse_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1825, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1858, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2067, in _parse_known_args
start_index = consume_optional(start_index)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2007, in consume_optional
take_action(action, args, option_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 1919, in take_action
argument_values = self._get_values(action, argument_strings)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2450, in _get_values
value = self._get_value(action, arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/argparse.py", line 2483, in _get_value
result = type_func(arg_string)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/commandlineparser.py", line 60, in gmx_MMPBSA_file
GMXMMPBSA_ERROR(f'{result} do not exist or is inaccessible')
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
md-nowat.tpr do not exist or is inaccessible
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[37672,1],3]
Exit code: 1
--------------------------------------------------------------------------
(gmxMMPBSA) mpirun -np 8 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
tets
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
tets
tets
tets
tets
tets
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Checking external programs...
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] Checking mmpbsa.in input file...
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] Checking external programs...Done.
[INFO ] Checking external programs...
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
tets
tets
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[ERROR ] MMPBSA_Error
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 289, in gmx2pdb
GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(comprog), self.FILES.complex_trajs[0]))
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[ERROR ] MMPBSA_Error
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
[ERROR ] MMPBSA_Error
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
[ERROR ] MMPBSA_Error
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 289, in gmx2pdb
GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(comprog), self.FILES.complex_trajs[0]))
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 289, in gmx2pdb
GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(comprog), self.FILES.complex_trajs[0]))
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 289, in gmx2pdb
GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(comprog), self.FILES.complex_trajs[0]))
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Checking the structures consistency...
[WARNING] No reference structure was found and the complex structure not contain any chain ID. Assigning chains ID automatically...
[INFO ]
[INFO ] Using topology conversion. Setting radiopt = 0...
[INFO ] Building Normal Complex Amber topology...
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
tops = self.gmxtop2prmtop()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 534, in gmxtop2prmtop
com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 822, in cleantop
rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
self.read(fname, defines, parametrize)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 289, in read
for line in f:
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_gromacsfile.py", line 44, in __iter__
for line in self._handle:
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 175, in __iter__
self._ppcmdmap[cmd](self, args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 30, in wrapper
return func(self, args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 288, in _pp_include
raise PreProcessorError('Could not find %s' % includefile)
PreProcessorError: Could not find Ligand.itp
Exiting. All files have been retained.
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Checking the structures consistency...
[WARNING] No reference structure was found and the complex structure not contain any chain ID. Assigning chains ID automatically...
[INFO ]
[INFO ] Using topology conversion. Setting radiopt = 0...
[INFO ] Building Normal Complex Amber topology...
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
tops = self.gmxtop2prmtop()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 534, in gmxtop2prmtop
com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 822, in cleantop
rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
self.read(fname, defines, parametrize)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 289, in read
for line in f:
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_gromacsfile.py", line 44, in __iter__
for line in self._handle:
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 175, in __iter__
self._ppcmdmap[cmd](self, args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 30, in wrapper
return func(self, args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 288, in _pp_include
raise PreProcessorError('Could not find %s' % includefile)
PreProcessorError: Could not find Ligand.itp
Exiting. All files have been retained.
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 521, in _parse_atom_parts
parts = cls._parse_atom_parts_1(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 512, in _parse_atom_parts_1
number=line[6:11], name=line[12:16].strip(), alternate_location=line[16].strip(),
IndexError: string index out of range
Exiting. All files have been retained.
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Checking the structures consistency...
[WARNING] No reference structure was found and the complex structure not contain any chain ID. Assigning chains ID automatically...
[INFO ]
[INFO ] Using topology conversion. Setting radiopt = 0...
[INFO ] Building Normal Complex Amber topology...
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
tops = self.gmxtop2prmtop()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 534, in gmxtop2prmtop
com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 822, in cleantop
rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
self.read(fname, defines, parametrize)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 289, in read
for line in f:
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_gromacsfile.py", line 44, in __iter__
for line in self._handle:
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 175, in __iter__
self._ppcmdmap[cmd](self, args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 30, in wrapper
return func(self, args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 288, in _pp_include
raise PreProcessorError('Could not find %s' % includefile)
PreProcessorError: Could not find Ligand.itp
Exiting. All files have been retained.
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[37906,1],6]
Exit code: 1
--------------------------------------------------------------------------
(gmxMMPBSA) mpirun -np 8 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 674, in make_prmtops
self.remove(-1)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1154, in remove
utils.remove(flag, fnpre=self.pre)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 715, in remove
os.remove(fil)
FileNotFoundError: [Errno 2] No such file or directory: '#_GMXMMPBSA_COM_index.ndx.1#'
Exiting. All files have been retained.
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
tets
tets
tets
tets
tets
tets
tets
[INFO ] Checking external programs...
[INFO ] Checking mmpbsa.in input file...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking external programs...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Checking mmpbsa.in input file...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking external programs...
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] Checking external programs...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] Checking external programs...
[INFO ] Checking external programs...
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] Checking external programs...Done.
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Making gmx_MMPBSA index for complex...
tets
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[ERROR ] MMPBSA_Error
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 289, in gmx2pdb
GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(comprog), self.FILES.complex_trajs[0]))
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 521, in _parse_atom_parts
parts = cls._parse_atom_parts_1(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 512, in _parse_atom_parts_1
number=line[6:11], name=line[12:16].strip(), alternate_location=line[16].strip(),
IndexError: string index out of range
Exiting. All files have been retained.
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 484, in gmx2pdb
self.receptor_str = self.molstr(self.receptor_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 523, in _parse_atom_parts
x=float(line[30:38]), y=float(line[38:46]), z=float(line[46:54]),
ValueError: could not convert string to float: '\x00\x00\x00\x00\x00\x00\x00\x00'
Exiting. All files have been retained.
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 484, in gmx2pdb
self.receptor_str = self.molstr(self.receptor_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 523, in _parse_atom_parts
x=float(line[30:38]), y=float(line[38:46]), z=float(line[46:54]),
ValueError: could not convert string to float: '\x00\x00\x00\x00\x00\x00\x00\x00'
Exiting. All files have been retained.
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 484, in gmx2pdb
self.receptor_str = self.molstr(self.receptor_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 523, in _parse_atom_parts
x=float(line[30:38]), y=float(line[38:46]), z=float(line[46:54]),
ValueError: could not convert string to float: '\x00\x00\x00\x00\x00\x00\x00\x00'
Exiting. All files have been retained.
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 523, in _parse_atom_parts
x=float(line[30:38]), y=float(line[38:46]), z=float(line[46:54]),
ValueError: could not convert string to float: ''
Exiting. All files have been retained.
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 523, in _parse_atom_parts
x=float(line[30:38]), y=float(line[38:46]), z=float(line[46:54]),
ValueError: could not convert string to float: ''
Exiting. All files have been retained.
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[38207,1],6]
Exit code: 1
--------------------------------------------------------------------------
(gmxMMPBSA) mpirun -np 8 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
tets
[INFO ] Starting gmx_MMPBSA v1.6.1
tets
tets
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking mmpbsa.in input file...
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
tets
tets
tets
tets
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 674, in make_prmtops
self.remove(-1)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1154, in remove
utils.remove(flag, fnpre=self.pre)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 715, in remove
os.remove(fil)
FileNotFoundError: [Errno 2] No such file or directory: '#_GMXMMPBSA_COM_index.ndx.1#'
Exiting. All files have been retained.
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 674, in make_prmtops
self.remove(-1)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1154, in remove
utils.remove(flag, fnpre=self.pre)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 715, in remove
os.remove(fil)
FileNotFoundError: [Errno 2] No such file or directory: '#_GMXMMPBSA_COM_index.ndx.3#'
Exiting. All files have been retained.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Checking external programs...Done.
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Making gmx_MMPBSA index for complex...
tets
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[ERROR ] MMPBSA_Error
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 289, in gmx2pdb
GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(comprog), self.FILES.complex_trajs[0]))
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
/home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying md-wh-nj-fit.xtc
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Checking the structures consistency...
[WARNING] No reference structure was found and the complex structure not contain any chain ID. Assigning chains ID automatically...
[INFO ]
[INFO ] Using topology conversion. Setting radiopt = 0...
[INFO ] Building Normal Complex Amber topology...
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
tops = self.gmxtop2prmtop()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 534, in gmxtop2prmtop
com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 822, in cleantop
rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
self.read(fname, defines, parametrize)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 461, in read
self.parametrize()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 1102, in parametrize
raise ParameterError('Not all improper torsion '
ParameterError: Not all improper torsion parameters found
Exiting. All files have been retained.
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Checking the structures consistency...
[WARNING] No reference structure was found and the complex structure not contain any chain ID. Assigning chains ID automatically...
[INFO ]
[INFO ] Using topology conversion. Setting radiopt = 0...
[INFO ] Building Normal Complex Amber topology...
[ERROR ] MMPBSA_Error
The atom 1537 in the complex index is not found in the topology file. Please check that the files are consistent.
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
tops = self.gmxtop2prmtop()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 534, in gmxtop2prmtop
com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 832, in cleantop
GMXMMPBSA_ERROR(f'The atom {i} in the {id} index is not found in the topology file. Please check that '
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
The atom 1537 in the complex index is not found in the topology file. Please check that the files are consistent.
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Checking the structures consistency...
[WARNING] No reference structure was found and the complex structure not contain any chain ID. Assigning chains ID automatically...
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 493, in gmx2pdb
self.check_structures(self.complex_str, self.receptor_str, self.ligand_str)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1305, in check_structures
self._assign_chains_IDs(com_str, rec_str, lig_str)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1333, in _assign_chains_IDs
rec_str.residues[i].chain = res.chain
IndexError: list index out of range
Exiting. All files have been retained.
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Checking the structures consistency...
[WARNING] No reference structure was found and the complex structure not contain any chain ID. Assigning chains ID automatically...
[INFO ]
[INFO ] Using topology conversion. Setting radiopt = 0...
[INFO ] Building Normal Complex Amber topology...
[ERROR ] MMPBSA_Error
The atom 299 in the complex index is not found in the topology file. Please check that the files are consistent.
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
tops = self.gmxtop2prmtop()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 534, in gmxtop2prmtop
com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 832, in cleantop
GMXMMPBSA_ERROR(f'The atom {i} in the {id} index is not found in the topology file. Please check that '
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
The atom 299 in the complex index is not found in the topology file. Please check that the files are consistent.
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 521, in _parse_atom_parts
parts = cls._parse_atom_parts_1(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 512, in _parse_atom_parts_1
number=line[6:11], name=line[12:16].strip(), alternate_location=line[16].strip(),
IndexError: string index out of range
Exiting. All files have been retained.
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[38887,1],3]
Exit code: 1
--------------------------------------------------------------------------
(gmxMMPBSA) mpirun -np 8 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
tets
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Making gmx_MMPBSA index for complex...
tets
tets
tets
tets
tets
tets
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Checking external programs...Done.
[INFO ] Checking mmpbsa.in input file...
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Making gmx_MMPBSA index for complex...
tets
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking mmpbsa.in input file...
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Checking external programs...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[ERROR ] MMPBSA_Error
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 487, in gmx2pdb
self.ref_str = check_str(self.FILES.reference_structure, ref=True)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 517, in check_str
GMXMMPBSA_ERROR('The reference structure used is inconsistent. The following residue does not have a '
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[ERROR ] MMPBSA_Error
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 487, in gmx2pdb
self.ref_str = check_str(self.FILES.reference_structure, ref=True)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 517, in check_str
GMXMMPBSA_ERROR('The reference structure used is inconsistent. The following residue does not have a '
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
[ERROR ] MMPBSA_Error
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 487, in gmx2pdb
self.ref_str = check_str(self.FILES.reference_structure, ref=True)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 517, in check_str
GMXMMPBSA_ERROR('The reference structure used is inconsistent. The following residue does not have a '
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[ERROR ] MMPBSA_Error
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 487, in gmx2pdb
self.ref_str = check_str(self.FILES.reference_structure, ref=True)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 517, in check_str
GMXMMPBSA_ERROR('The reference structure used is inconsistent. The following residue does not have a '
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[ERROR ] MMPBSA_Error
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 487, in gmx2pdb
self.ref_str = check_str(self.FILES.reference_structure, ref=True)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 517, in check_str
GMXMMPBSA_ERROR('The reference structure used is inconsistent. The following residue does not have a '
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[ERROR ] MMPBSA_Error
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 487, in gmx2pdb
self.ref_str = check_str(self.FILES.reference_structure, ref=True)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 517, in check_str
GMXMMPBSA_ERROR('The reference structure used is inconsistent. The following residue does not have a '
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[ERROR ] MMPBSA_Error
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 487, in gmx2pdb
self.ref_str = check_str(self.FILES.reference_structure, ref=True)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 517, in check_str
GMXMMPBSA_ERROR('The reference structure used is inconsistent. The following residue does not have a '
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[ERROR ] MMPBSA_Error
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 487, in gmx2pdb
self.ref_str = check_str(self.FILES.reference_structure, ref=True)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 517, in check_str
GMXMMPBSA_ERROR('The reference structure used is inconsistent. The following residue does not have a '
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
The reference structure used is inconsistent. The following residue does not have a chain ID: 1:ALA
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[38948,1],4]
Exit code: 1
--------------------------------------------------------------------------
(gmxMMPBSA) mpirun -np 8 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
tets
tets
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[ERROR ] MMPBSA_Error
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 869, in get_cl_args
utils._get_dup_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 469, in _get_dup_args
GMXMMPBSA_ERROR('Several args are duplicated in the command-line...\n'
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Starting gmx_MMPBSA v1.6.1
[ERROR ] MMPBSA_Error
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 869, in get_cl_args
utils._get_dup_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 469, in _get_dup_args
GMXMMPBSA_ERROR('Several args are duplicated in the command-line...\n'
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
tets
[ERROR ] MMPBSA_Error
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
tets
tets
tets
tets
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 869, in get_cl_args
utils._get_dup_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 469, in _get_dup_args
GMXMMPBSA_ERROR('Several args are duplicated in the command-line...\n'
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[ERROR ] MMPBSA_Error
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 869, in get_cl_args
utils._get_dup_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 469, in _get_dup_args
GMXMMPBSA_ERROR('Several args are duplicated in the command-line...\n'
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[ERROR ] MMPBSA_Error
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
[ERROR ] MMPBSA_Error
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 869, in get_cl_args
utils._get_dup_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 469, in _get_dup_args
GMXMMPBSA_ERROR('Several args are duplicated in the command-line...\n'
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[ERROR ] MMPBSA_Error
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 869, in get_cl_args
utils._get_dup_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 469, in _get_dup_args
GMXMMPBSA_ERROR('Several args are duplicated in the command-line...\n'
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 869, in get_cl_args
utils._get_dup_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 469, in _get_dup_args
GMXMMPBSA_ERROR('Several args are duplicated in the command-line...\n'
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2 -cr 0ns.pdb
tets
[ERROR ] MMPBSA_Error
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 64, in gmxmmpbsa
app.get_cl_args(sys.argv[1:])
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 869, in get_cl_args
utils._get_dup_args(args)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 469, in _get_dup_args
GMXMMPBSA_ERROR('Several args are duplicated in the command-line...\n'
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:
Several args are duplicated in the command-line...
Duplicated args:
-cs 0ns.pdb <---> -cr 0ns.pdb
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[39207,1],2]
Exit code: 1
--------------------------------------------------------------------------
(gmxMMPBSA) mpirun -np 8 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
tets
tets
tets
tets
tets
tets
tets
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 674, in make_prmtops
self.remove(-1)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1154, in remove
utils.remove(flag, fnpre=self.pre)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 715, in remove
os.remove(fil)
FileNotFoundError: [Errno 2] No such file or directory: '#_GMXMMPBSA_REC.pdb.7#'
Exiting. All files have been retained.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 674, in make_prmtops
self.remove(-1)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1154, in remove
utils.remove(flag, fnpre=self.pre)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 715, in remove
os.remove(fil)
FileNotFoundError: [Errno 2] No such file or directory: '#_GMXMMPBSA_REC.pdb.7#'
Exiting. All files have been retained.
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
tets
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs 0ns.pdb -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking mmpbsa.in input file...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] Checking mmpbsa.in input file...
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 523, in _parse_atom_parts
x=float(line[30:38]), y=float(line[38:46]), z=float(line[46:54]),
ValueError: could not convert string to float: '\x00\x00\x00\x00\x00\x00\x00\x00'
Exiting. All files have been retained.
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 383, in parse
inst.struct.assign_bonds()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/structure.py", line 976, in assign_bonds
pairs = find_atom_pairs(self, mindist, unassigned_atoms)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/utils/pairlist.py", line 39, in find_atom_pairs
voxels = np.array((coords - coords.min(axis=0)) / dist, dtype=int)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/numpy/core/_methods.py", line 45, in _amin
return umr_minimum(a, axis, None, out, keepdims, initial, where)
ValueError: zero-size array to reduction operation minimum which has no identity
Exiting. All files have been retained.
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 523, in _parse_atom_parts
x=float(line[30:38]), y=float(line[38:46]), z=float(line[46:54]),
ValueError: could not convert string to float: '\x00\x00\x00\x00\x00\x00\x00\x00'
Exiting. All files have been retained.
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 523, in _parse_atom_parts
x=float(line[30:38]), y=float(line[38:46]), z=float(line[46:54]),
ValueError: could not convert string to float: '\x00\x00\x00\x00\x00\x00\x00\x00'
Exiting. All files have been retained.
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
inst._parse_open_file(fileobj)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
method_dispatch[rec](line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 624, in _parse_atom_record
atom_parts = self._parse_atom_parts(line)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 523, in _parse_atom_parts
x=float(line[30:38]), y=float(line[38:46]), z=float(line[46:54]),
ValueError: could not convert string to float: '\x00\x00\x00\x00\x00\x00\x00\x00'
Exiting. All files have been retained.
[INFO ] Generating ligand parameters from Ligand_user_gaff2.mol2 file...
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 483, in gmx2pdb
self.complex_str = self.molstr(self.complex_str_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1402, in molstr
structure = parmed.read_PDB(pdb_file)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/formats/pdb.py", line 383, in parse
inst.struct.assign_bonds()
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/structure.py", line 976, in assign_bonds
pairs = find_atom_pairs(self, mindist, unassigned_atoms)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/utils/pairlist.py", line 39, in find_atom_pairs
voxels = np.array((coords - coords.min(axis=0)) / dist, dtype=int)
File "/home/drazzam/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/numpy/core/_methods.py", line 45, in _amin
return umr_minimum(a, axis, None, out, keepdims, initial, where)
ValueError: zero-size array to reduction operation minimum which has no identity
Exiting. All files have been retained.
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[39568,1],3]
Exit code: 1
--------------------------------------------------------------------------
(gmxMMPBSA)
Mario Sergio Valdes
May 15, 2023, 2:14:37 PM5/15/23
to gmx_MMPBSA
This is an inconsistent behavor, probably because the mpi4py package is not installed.
Please, show me the output of "conda list"
Faizul Azam
May 15, 2023, 4:04:06 PM5/15/23
to gmx_MMPBSA
Thanks for your prompt reply. Here is the list:
(base) conda list
# packages in environment at /home/drazzam/anaconda3:
#
# Name Version Build Channel
_ipyw_jlab_nb_ext_conf 0.1.0 py39h06a4308_1
_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
alabaster 0.7.12 pyhd3eb1b0_0
anaconda 2022.10 py39_0
anaconda-client 1.11.0 py39h06a4308_0
anaconda-navigator 2.3.1 py39h06a4308_0
anaconda-project 0.11.1 py39h06a4308_0
anyio 3.5.0 py39h06a4308_0
appdirs 1.4.4 pyhd3eb1b0_0
argon2-cffi 21.3.0 pyhd3eb1b0_0
argon2-cffi-bindings 21.2.0 py39h7f8727e_0
arrow 1.2.2 pyhd3eb1b0_0
astroid 2.11.7 py39h06a4308_0
astropy 5.1 py39h7deecbd_0
atomicwrites 1.4.0 py_0
attrs 21.4.0 pyhd3eb1b0_0
automat 20.2.0 py_0
autopep8 1.6.0 pyhd3eb1b0_1
babel 2.9.1 pyhd3eb1b0_0
backcall 0.2.0 pyhd3eb1b0_0
backports 1.1 pyhd3eb1b0_0
backports.functools_lru_cache 1.6.4 pyhd3eb1b0_0
backports.tempfile 1.0 pyhd3eb1b0_1
backports.weakref 1.0.post1 py_1
bcrypt 3.2.0 py39h5eee18b_1
beautifulsoup4 4.11.1 py39h06a4308_0
binaryornot 0.4.4 pyhd3eb1b0_1
biopython 1.81 pypi_0 pypi
bitarray 2.5.1 py39h5eee18b_0
bkcharts 0.2 py39h06a4308_1
black 22.6.0 py39h06a4308_0
blas 1.0 mkl
bleach 4.1.0 pyhd3eb1b0_0
blosc 1.21.0 h4ff587b_1
bokeh 2.4.3 py39h06a4308_0
boto3 1.24.28 py39h06a4308_0
botocore 1.27.28 py39h06a4308_0
bottleneck 1.3.5 py39h7deecbd_0
brotli 1.0.9 h5eee18b_7
brotli-bin 1.0.9 h5eee18b_7
brotlipy 0.7.0 py39h27cfd23_1003
brunsli 0.1 h2531618_0
bzip2 1.0.8 h7b6447c_0
c-ares 1.18.1 h7f8727e_0
ca-certificates 2022.07.19 h06a4308_0
cairo 1.16.0 h19f5f5c_2
certifi 2022.9.14 py39h06a4308_0
cffi 1.15.1 py39h74dc2b5_0
cfitsio 3.470 h5893167_7
chardet 4.0.0 py39h06a4308_1003
charls 2.2.0 h2531618_0
charset-normalizer 2.0.4 pyhd3eb1b0_0
click 8.0.4 py39h06a4308_0
cloudpickle 2.0.0 pyhd3eb1b0_0
clyent 1.2.2 py39h06a4308_1
colorama 0.4.5 py39h06a4308_0
colorcet 3.0.0 py39h06a4308_0
conda 22.9.0 py39hf3d152e_2 conda-forge
conda-build 3.22.0 py39h06a4308_0
conda-content-trust 0.1.3 py39h06a4308_0
conda-env 2.6.0 1
conda-pack 0.6.0 pyhd3eb1b0_0
conda-package-handling 1.9.0 py39h5eee18b_0
conda-repo-cli 1.0.20 py39h06a4308_0
conda-token 0.4.0 pyhd3eb1b0_0
conda-verify 3.4.2 py_1
constantly 15.1.0 pyh2b92418_0
cookiecutter 1.7.3 pyhd3eb1b0_0
cryptography 37.0.1 py39h9ce1e76_0
cssselect 1.1.0 pyhd3eb1b0_0
cuda 11.8.0 0 nvidia
cuda-cccl 11.8.89 0 nvidia
cuda-command-line-tools 11.8.0 0 nvidia
cuda-compiler 11.8.0 0 nvidia
cuda-cudart 11.8.89 0 nvidia
cuda-cudart-dev 11.8.89 0 nvidia
cuda-cuobjdump 11.8.86 0 nvidia
cuda-cupti 11.8.87 0 nvidia
cuda-cuxxfilt 11.8.86 0 nvidia
cuda-demo-suite 11.8.86 0 nvidia
cuda-documentation 11.8.86 0 nvidia
cuda-driver-dev 11.8.89 0 nvidia
cuda-gdb 11.8.86 0 nvidia
cuda-libraries 11.8.0 0 nvidia
cuda-libraries-dev 11.8.0 0 nvidia
cuda-memcheck 11.8.86 0 nvidia
cuda-nsight 11.8.86 0 nvidia
cuda-nsight-compute 11.8.0 0 nvidia
cuda-nvcc 11.8.89 0 nvidia
cuda-nvdisasm 11.8.86 0 nvidia
cuda-nvml-dev 11.8.86 0 nvidia
cuda-nvprof 11.8.87 0 nvidia
cuda-nvprune 11.8.86 0 nvidia
cuda-nvrtc 11.8.89 0 nvidia
cuda-nvrtc-dev 11.8.89 0 nvidia
cuda-nvtx 11.8.86 0 nvidia
cuda-nvvp 11.8.87 0 nvidia
cuda-profiler-api 11.8.86 0 nvidia
cuda-runtime 11.8.0 0 nvidia
cuda-sanitizer-api 11.8.86 0 nvidia
cuda-toolkit 11.8.0 0 nvidia
cuda-tools 11.8.0 0 nvidia
cuda-visual-tools 11.8.0 0 nvidia
curl 7.84.0 h5eee18b_0
cycler 0.11.0 pyhd3eb1b0_0
cython 0.29.32 py39h6a678d5_0
cytoolz 0.11.0 py39h27cfd23_0
daal4py 2021.6.0 py39h79cecc1_1
dal 2021.6.0 hdb19cb5_916
dask 2022.7.0 py39h06a4308_0
dask-core 2022.7.0 py39h06a4308_0
dataclasses 0.8 pyh6d0b6a4_7
datashader 0.14.1 py39h06a4308_0
datashape 0.5.4 py39h06a4308_1
dbus 1.13.18 hb2f20db_0
debugpy 1.5.1 py39h295c915_0
decorator 5.1.1 pyhd3eb1b0_0
defusedxml 0.7.1 pyhd3eb1b0_0
diff-match-patch 20200713 pyhd3eb1b0_0
dill 0.3.4 pyhd3eb1b0_0
distributed 2022.7.0 py39h06a4308_0
docutils 0.18.1 py39h06a4308_3
entrypoints 0.4 py39h06a4308_0
et_xmlfile 1.1.0 py39h06a4308_0
expat 2.4.9 h6a678d5_0
fasteners 0.18 pypi_0 pypi
fftw 3.3.9 h27cfd23_1
filelock 3.6.0 pyhd3eb1b0_0
flake8 4.0.1 pyhd3eb1b0_1
flask 1.1.2 pyhd3eb1b0_0
fontconfig 2.13.1 h6c09931_0
fonttools 4.25.0 pyhd3eb1b0_0
freetype 2.11.0 h70c0345_0
fsspec 2022.7.1 py39h06a4308_0
future 0.18.2 py39h06a4308_1
gds-tools 1.4.0.31 0 nvidia
gensim 4.1.2 py39h295c915_0
giflib 5.2.1 h7b6447c_0
glib 2.69.1 h4ff587b_1
glob2 0.7 pyhd3eb1b0_0
gmp 6.2.1 h295c915_3
gmpy2 2.1.2 py39heeb90bb_0
greenlet 1.1.1 py39h295c915_0
griddataformats 1.0.1 pypi_0 pypi
gsd 2.8.1 pypi_0 pypi
gst-plugins-base 1.14.0 h8213a91_2
gstreamer 1.14.0 h28cd5cc_2
h5py 3.7.0 py39h737f45e_0
hdf5 1.10.6 h3ffc7dd_1
hdf5-1107 1.10.7 0 salilab
heapdict 1.0.1 pyhd3eb1b0_0
holoviews 1.15.0 py39h06a4308_0
hvplot 0.8.0 py39h06a4308_0
hyperlink 21.0.0 pyhd3eb1b0_0
icu 58.2 he6710b0_3
idna 3.3 pyhd3eb1b0_0
imagecodecs 2021.8.26 py39hf0132c2_1
imageio 2.19.3 py39h06a4308_0
imagesize 1.4.1 py39h06a4308_0
importlib-metadata 4.11.3 py39h06a4308_0
importlib_metadata 4.11.3 hd3eb1b0_0
incremental 21.3.0 pyhd3eb1b0_0
inflection 0.5.1 py39h06a4308_0
iniconfig 1.1.1 pyhd3eb1b0_0
intake 0.6.5 pyhd3eb1b0_0
intel-openmp 2021.4.0 h06a4308_3561
intervaltree 3.1.0 pyhd3eb1b0_0
ipykernel 6.15.2 py39h06a4308_0
ipython 7.31.1 py39h06a4308_1
ipython_genutils 0.2.0 pyhd3eb1b0_1
ipywidgets 7.6.5 pyhd3eb1b0_1
isort 5.9.3 pyhd3eb1b0_0
itemadapter 0.3.0 pyhd3eb1b0_0
itemloaders 1.0.4 pyhd3eb1b0_1
itsdangerous 2.0.1 pyhd3eb1b0_0
jdcal 1.4.1 pyhd3eb1b0_0
jedi 0.18.1 py39h06a4308_1
jeepney 0.7.1 pyhd3eb1b0_0
jellyfish 0.9.0 py39h7f8727e_0
jinja2 2.11.3 pyhd3eb1b0_0
jinja2-time 0.2.0 pyhd3eb1b0_3
jmespath 0.10.0 pyhd3eb1b0_0
joblib 1.1.0 pyhd3eb1b0_0
jpeg 9e h7f8727e_0
jq 1.6 h27cfd23_1000
json5 0.9.6 pyhd3eb1b0_0
jsonschema 4.16.0 py39h06a4308_0
jupyter 1.0.0 py39h06a4308_8
jupyter_client 7.3.4 py39h06a4308_0
jupyter_console 6.4.3 pyhd3eb1b0_0
jupyter_core 4.11.1 py39h06a4308_0
jupyter_server 1.18.1 py39h06a4308_0
jupyterlab 3.4.4 py39h06a4308_0
jupyterlab_pygments 0.1.2 py_0
jupyterlab_server 2.10.3 pyhd3eb1b0_1
jupyterlab_widgets 1.0.0 pyhd3eb1b0_1
jxrlib 1.1 h7b6447c_2
keyring 23.4.0 py39h06a4308_0
kiwisolver 1.4.2 py39h295c915_0
krb5 1.19.2 hac12032_0
lazy-object-proxy 1.6.0 py39h27cfd23_0
lcms2 2.12 h3be6417_0
ld_impl_linux-64 2.38 h1181459_1
lerc 3.0 h295c915_0
libaec 1.0.4 he6710b0_1
libarchive 3.6.1 hab531cd_0
libbrotlicommon 1.0.9 h5eee18b_7
libbrotlidec 1.0.9 h5eee18b_7
libbrotlienc 1.0.9 h5eee18b_7
libclang 10.0.1 default_hb85057a_2
libcublas 11.11.3.6 0 nvidia
libcublas-dev 11.11.3.6 0 nvidia
libcufft 10.9.0.58 0 nvidia
libcufft-dev 10.9.0.58 0 nvidia
libcufile 1.4.0.31 0 nvidia
libcufile-dev 1.4.0.31 0 nvidia
libcurand 10.3.0.86 0 nvidia
libcurand-dev 10.3.0.86 0 nvidia
libcurl 7.84.0 h91b91d3_0
libcusolver 11.4.1.48 0 nvidia
libcusolver-dev 11.4.1.48 0 nvidia
libcusparse 11.7.5.86 0 nvidia
libcusparse-dev 11.7.5.86 0 nvidia
libdeflate 1.8 h7f8727e_5
libedit 3.1.20210910 h7f8727e_0
libev 4.33 h7f8727e_1
libevent 2.1.12 h8f2d780_0
libffi 3.3 he6710b0_2
libgcc-ng 11.2.0 h1234567_1
libgfortran-ng 11.2.0 h00389a5_1
libgfortran5 11.2.0 h1234567_1
libgomp 11.2.0 h1234567_1
libidn2 2.3.2 h7f8727e_0
liblief 0.11.5 h295c915_1
libllvm10 10.0.1 hbcb73fb_5
libllvm11 11.1.0 h9e868ea_5
libnghttp2 1.46.0 hce63b2e_0
libnpp 11.8.0.86 0 nvidia
libnpp-dev 11.8.0.86 0 nvidia
libnvjpeg 11.9.0.86 0 nvidia
libnvjpeg-dev 11.9.0.86 0 nvidia
libpng 1.6.37 hbc83047_0
libpq 12.9 h16c4e8d_3
libsodium 1.0.18 h7b6447c_0
libspatialindex 1.9.3 h2531618_0
libssh2 1.10.0 h8f2d780_0
libstdcxx-ng 11.2.0 h1234567_1
libtiff 4.4.0 hecacb30_0
libunistring 0.9.10 h27cfd23_0
libuuid 1.0.3 h7f8727e_2
libwebp 1.2.2 h55f646e_0
libwebp-base 1.2.2 h7f8727e_0
libxcb 1.15 h7f8727e_0
libxkbcommon 1.0.1 hfa300c1_0
libxml2 2.9.14 h74e7548_0
libxslt 1.1.35 h4e12654_0
libzopfli 1.0.3 he6710b0_0
llvmlite 0.38.0 py39h4ff587b_0
locket 1.0.0 py39h06a4308_0
lxml 4.9.1 py39h1edc446_0
lz4 3.1.3 py39h27cfd23_0
lz4-c 1.9.3 h295c915_1
lzo 2.10 h7b6447c_2
markdown 3.3.4 py39h06a4308_0
markupsafe 2.0.1 py39h27cfd23_0
matplotlib 3.5.2 py39h06a4308_0
matplotlib-base 3.5.2 py39hf590b9c_0
matplotlib-inline 0.1.6 py39h06a4308_0
mccabe 0.7.0 pyhd3eb1b0_0
mdanalysis 2.4.3 pypi_0 pypi
mistune 0.8.4 py39h27cfd23_1000
mkl 2021.4.0 h06a4308_640
mkl-service 2.4.0 py39h7f8727e_0
mkl_fft 1.3.1 py39hd3c417c_0
mkl_random 1.2.2 py39h51133e4_0
mmtf-python 1.1.3 pypi_0 pypi
mock 4.0.3 pyhd3eb1b0_0
modeller 10.4 py39h9bf148f_0 salilab
mpc 1.1.0 h10f8cd9_1
mpfr 4.0.2 hb69a4c5_1
mpi 1.0 mpich
mpich 3.3.2 external_0
mpmath 1.2.1 py39h06a4308_0
mrcfile 1.4.3 pypi_0 pypi
msgpack-python 1.0.3 py39hd09550d_0
multipledispatch 0.6.0 py39h06a4308_0
munkres 1.1.4 py_0
mypy_extensions 0.4.3 py39h06a4308_1
navigator-updater 0.3.0 py39h06a4308_0
nbclassic 0.3.5 pyhd3eb1b0_0
nbclient 0.5.13 py39h06a4308_0
nbconvert 6.4.4 py39h06a4308_0
nbformat 5.5.0 py39h06a4308_0
ncurses 6.3 h5eee18b_3
nest-asyncio 1.5.5 py39h06a4308_0
networkx 2.8.4 py39h06a4308_0
nltk 3.7 pyhd3eb1b0_0
nose 1.3.7 pyhd3eb1b0_1008
notebook 6.4.12 py39h06a4308_0
nsight-compute 2022.3.0.22 0 nvidia
nspr 4.33 h295c915_0
nss 3.74 h0370c37_0
numba 0.55.1 py39h51133e4_0
numexpr 2.8.3 py39h807cd23_0
numpy 1.21.5 py39h6c91a56_3
numpy-base 1.21.5 py39ha15fc14_3
numpydoc 1.4.0 py39h06a4308_0
olefile 0.46 pyhd3eb1b0_0
oniguruma 6.9.7.1 h27cfd23_0
openbabel 3.1.1 py39hee2736e_2 conda-forge
openjpeg 2.4.0 h3ad879b_0
openpyxl 3.0.10 py39h5eee18b_0
openssl 1.1.1q h7f8727e_0
packaging 21.3 pyhd3eb1b0_0
pandas 1.4.4 py39h6a678d5_0
pandocfilters 1.5.0 pyhd3eb1b0_0
panel 0.13.1 py39h06a4308_0
param 1.12.0 pyhd3eb1b0_0
parsel 1.6.0 py39h06a4308_0
parso 0.8.3 pyhd3eb1b0_0
partd 1.2.0 pyhd3eb1b0_1
patch 2.7.6 h7b6447c_1001
patchelf 0.13 h295c915_0
pathlib 1.0.1 pyhd3eb1b0_1
pathspec 0.9.0 py39h06a4308_0
patsy 0.5.2 py39h06a4308_1
pcre 8.45 h295c915_0
pep8 1.7.1 py39h06a4308_1
pexpect 4.8.0 pyhd3eb1b0_3
pickleshare 0.7.5 pyhd3eb1b0_1003
pillow 9.2.0 py39hace64e9_1
pip 22.2.2 py39h06a4308_0
pixman 0.40.0 h36c2ea0_0 conda-forge
pkginfo 1.8.2 pyhd3eb1b0_0
platformdirs 2.5.2 py39h06a4308_0
plotly 5.9.0 py39h06a4308_0
pluggy 1.0.0 py39h06a4308_1
ply 3.11 py39h06a4308_0
poyo 0.5.0 pyhd3eb1b0_0
prometheus_client 0.14.1 py39h06a4308_0
prompt-toolkit 3.0.20 pyhd3eb1b0_0
prompt_toolkit 3.0.20 hd3eb1b0_0
protego 0.1.16 py_0
psutil 5.9.0 py39h5eee18b_0
ptyprocess 0.7.0 pyhd3eb1b0_2
py 1.11.0 pyhd3eb1b0_0
py-lief 0.11.5 py39h295c915_1
pyasn1 0.4.8 pyhd3eb1b0_0
pyasn1-modules 0.2.8 py_0
pycodestyle 2.8.0 pyhd3eb1b0_0
pycosat 0.6.3 py39h27cfd23_0
pycparser 2.21 pyhd3eb1b0_0
pyct 0.4.8 py39h06a4308_1
pycurl 7.45.1 py39h8f2d780_0
pydispatcher 2.0.5 py39h06a4308_2
pydocstyle 6.1.1 pyhd3eb1b0_0
pyerfa 2.0.0 py39h27cfd23_0
pyflakes 2.4.0 pyhd3eb1b0_0
pygments 2.11.2 pyhd3eb1b0_0
pyhamcrest 2.0.2 pyhd3eb1b0_2
pyjwt 2.4.0 py39h06a4308_0
pylint 2.14.5 py39h06a4308_0
pyls-spyder 0.4.0 pyhd3eb1b0_0
pyodbc 4.0.34 py39h6a678d5_0
pyopenssl 22.0.0 pyhd3eb1b0_0
pyparsing 3.0.9 py39h06a4308_0
pyqt 5.15.7 py39h6a678d5_1
pyqt5-sip 12.11.0 py39h6a678d5_1
pyqtwebengine 5.15.7 py39h6a678d5_1
pyrsistent 0.18.0 py39heee7806_0
pysocks 1.7.1 py39h06a4308_0
pytables 3.6.1 py39h77479fe_1
pytest 7.1.2 py39h06a4308_0
python 3.9.13 haa1d7c7_1
python-dateutil 2.8.2 pyhd3eb1b0_0
python-fastjsonschema 2.16.2 py39h06a4308_0
python-libarchive-c 2.9 pyhd3eb1b0_1
python-lsp-black 1.2.1 py39h06a4308_0
python-lsp-jsonrpc 1.0.0 pyhd3eb1b0_0
python-lsp-server 1.5.0 py39h06a4308_0
python-slugify 5.0.2 pyhd3eb1b0_0
python-snappy 0.6.0 py39h2531618_3
python_abi 3.9 2_cp39 conda-forge
pytz 2022.1 py39h06a4308_0
pyviz_comms 2.0.2 pyhd3eb1b0_0
pywavelets 1.3.0 py39h7f8727e_0
pyxdg 0.27 pyhd3eb1b0_0
pyyaml 6.0 py39h7f8727e_1
pyzmq 23.2.0 py39h6a678d5_0
qdarkstyle 3.0.2 pyhd3eb1b0_0
qstylizer 0.1.10 pyhd3eb1b0_0
qt 5.15.9 h06a4308_0
qt-main 5.15.2 h327a75a_7
qt-webengine 5.15.9 hd2b0992_4
qtawesome 1.0.3 pyhd3eb1b0_0
qtconsole 5.3.2 py39h06a4308_0
qtpy 2.2.0 py39h06a4308_0
qtwebkit 5.212 h4eab89a_4
queuelib 1.5.0 py39h06a4308_0
readline 8.1.2 h7f8727e_1
regex 2022.7.9 py39h5eee18b_0
requests 2.28.1 py39h06a4308_0
requests-file 1.5.1 pyhd3eb1b0_0
ripgrep 13.0.0 hbdeaff8_0
rope 0.22.0 pyhd3eb1b0_0
rtree 0.9.7 py39h06a4308_1
ruamel_yaml 0.15.100 py39h27cfd23_0
s3transfer 0.6.0 py39h06a4308_0
scikit-image 0.19.2 py39h51133e4_0
scikit-learn 1.0.2 py39h51133e4_1
scikit-learn-intelex 2021.6.0 py39h06a4308_0
scipy 1.9.1 py39h14f4228_0
scrapy 2.6.2 py39h06a4308_0
seaborn 0.11.2 pyhd3eb1b0_0
secretstorage 3.3.1 py39h06a4308_0
send2trash 1.8.0 pyhd3eb1b0_1
service_identity 18.1.0 pyhd3eb1b0_1
setuptools 63.4.1 py39h06a4308_0
sip 6.6.2 py39h6a678d5_0
six 1.16.0 pyhd3eb1b0_1
smart_open 5.2.1 py39h06a4308_0
snappy 1.1.9 h295c915_0
sniffio 1.2.0 py39h06a4308_1
snowballstemmer 2.2.0 pyhd3eb1b0_0
sortedcollections 2.1.0 pyhd3eb1b0_0
sortedcontainers 2.4.0 pyhd3eb1b0_0
soupsieve 2.3.1 pyhd3eb1b0_0
sphinx 5.0.2 py39h06a4308_0
sphinxcontrib-applehelp 1.0.2 pyhd3eb1b0_0
sphinxcontrib-devhelp 1.0.2 pyhd3eb1b0_0
sphinxcontrib-htmlhelp 2.0.0 pyhd3eb1b0_0
sphinxcontrib-jsmath 1.0.1 pyhd3eb1b0_0
sphinxcontrib-qthelp 1.0.3 pyhd3eb1b0_0
sphinxcontrib-serializinghtml 1.1.5 pyhd3eb1b0_0
spyder 5.3.3 py39h06a4308_0
spyder-kernels 2.3.3 py39h06a4308_0
sqlalchemy 1.4.39 py39h5eee18b_0
sqlite 3.39.3 h5082296_0
statsmodels 0.13.2 py39h7f8727e_0
sympy 1.10.1 py39h06a4308_0
tabulate 0.8.10 py39h06a4308_0
tbb 2021.6.0 hdb19cb5_0
tbb4py 2021.6.0 py39hdb19cb5_0
tblib 1.7.0 pyhd3eb1b0_0
tenacity 8.0.1 py39h06a4308_1
terminado 0.13.1 py39h06a4308_0
testpath 0.6.0 py39h06a4308_0
text-unidecode 1.3 pyhd3eb1b0_0
textdistance 4.2.1 pyhd3eb1b0_0
threadpoolctl 2.2.0 pyh0d69192_0
three-merge 0.1.1 pyhd3eb1b0_0
tifffile 2021.7.2 pyhd3eb1b0_2
tinycss 0.4 pyhd3eb1b0_1002
tk 8.6.12 h1ccaba5_0
tldextract 3.2.0 pyhd3eb1b0_0
toml 0.10.2 pyhd3eb1b0_0
tomli 2.0.1 py39h06a4308_0
tomlkit 0.11.1 py39h06a4308_0
toolz 0.11.2 pyhd3eb1b0_0
tornado 6.1 py39h27cfd23_0
tqdm 4.64.1 py39h06a4308_0
traitlets 5.1.1 pyhd3eb1b0_0
twisted 22.2.0 py39h5eee18b_1
typing-extensions 4.3.0 py39h06a4308_0
typing_extensions 4.3.0 py39h06a4308_0
tzdata 2022c h04d1e81_0
ujson 5.4.0 py39h6a678d5_0
unidecode 1.2.0 pyhd3eb1b0_0
unixodbc 2.3.11 h5eee18b_0
urllib3 1.26.11 py39h06a4308_0
w3lib 1.21.0 pyhd3eb1b0_0
watchdog 2.1.6 py39h06a4308_0
wcwidth 0.2.5 pyhd3eb1b0_0
webencodings 0.5.1 py39h06a4308_1
websocket-client 0.58.0 py39h06a4308_4
werkzeug 2.0.3 pyhd3eb1b0_0
wget 1.21.3 h0b77cf5_0
whatthepatch 1.0.2 py39h06a4308_0
wheel 0.37.1 pyhd3eb1b0_0
widgetsnbextension 3.5.2 py39h06a4308_0
wrapt 1.14.1 py39h5eee18b_0
wurlitzer 3.0.2 py39h06a4308_0
xarray 0.20.1 pyhd3eb1b0_1
xlrd 2.0.1 pyhd3eb1b0_0
xlsxwriter 3.0.3 pyhd3eb1b0_0
xz 5.2.6 h5eee18b_0
yaml 0.2.5 h7b6447c_0
yapf 0.31.0 pyhd3eb1b0_0
zeromq 4.3.4 h2531618_0
zfp 0.5.5 h295c915_6
zict 2.1.0 py39h06a4308_0
zipp 3.8.0 py39h06a4308_0
zlib 1.2.12 h5eee18b_3
zope 1.0 py39h06a4308_1
zope.interface 5.4.0 py39h7f8727e_0
zstd 1.5.2 ha4553b6_0
(base)
# packages in environment at /home/drazzam/anaconda3:
#
# Name Version Build Channel
_ipyw_jlab_nb_ext_conf 0.1.0 py39h06a4308_1
_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
alabaster 0.7.12 pyhd3eb1b0_0
anaconda 2022.10 py39_0
anaconda-client 1.11.0 py39h06a4308_0
anaconda-navigator 2.3.1 py39h06a4308_0
anaconda-project 0.11.1 py39h06a4308_0
anyio 3.5.0 py39h06a4308_0
appdirs 1.4.4 pyhd3eb1b0_0
argon2-cffi 21.3.0 pyhd3eb1b0_0
argon2-cffi-bindings 21.2.0 py39h7f8727e_0
arrow 1.2.2 pyhd3eb1b0_0
astroid 2.11.7 py39h06a4308_0
astropy 5.1 py39h7deecbd_0
atomicwrites 1.4.0 py_0
attrs 21.4.0 pyhd3eb1b0_0
automat 20.2.0 py_0
autopep8 1.6.0 pyhd3eb1b0_1
babel 2.9.1 pyhd3eb1b0_0
backcall 0.2.0 pyhd3eb1b0_0
backports 1.1 pyhd3eb1b0_0
backports.functools_lru_cache 1.6.4 pyhd3eb1b0_0
backports.tempfile 1.0 pyhd3eb1b0_1
backports.weakref 1.0.post1 py_1
bcrypt 3.2.0 py39h5eee18b_1
beautifulsoup4 4.11.1 py39h06a4308_0
binaryornot 0.4.4 pyhd3eb1b0_1
biopython 1.81 pypi_0 pypi
bitarray 2.5.1 py39h5eee18b_0
bkcharts 0.2 py39h06a4308_1
black 22.6.0 py39h06a4308_0
blas 1.0 mkl
bleach 4.1.0 pyhd3eb1b0_0
blosc 1.21.0 h4ff587b_1
bokeh 2.4.3 py39h06a4308_0
boto3 1.24.28 py39h06a4308_0
botocore 1.27.28 py39h06a4308_0
bottleneck 1.3.5 py39h7deecbd_0
brotli 1.0.9 h5eee18b_7
brotli-bin 1.0.9 h5eee18b_7
brotlipy 0.7.0 py39h27cfd23_1003
brunsli 0.1 h2531618_0
bzip2 1.0.8 h7b6447c_0
c-ares 1.18.1 h7f8727e_0
ca-certificates 2022.07.19 h06a4308_0
cairo 1.16.0 h19f5f5c_2
certifi 2022.9.14 py39h06a4308_0
cffi 1.15.1 py39h74dc2b5_0
cfitsio 3.470 h5893167_7
chardet 4.0.0 py39h06a4308_1003
charls 2.2.0 h2531618_0
charset-normalizer 2.0.4 pyhd3eb1b0_0
click 8.0.4 py39h06a4308_0
cloudpickle 2.0.0 pyhd3eb1b0_0
clyent 1.2.2 py39h06a4308_1
colorama 0.4.5 py39h06a4308_0
colorcet 3.0.0 py39h06a4308_0
conda 22.9.0 py39hf3d152e_2 conda-forge
conda-build 3.22.0 py39h06a4308_0
conda-content-trust 0.1.3 py39h06a4308_0
conda-env 2.6.0 1
conda-pack 0.6.0 pyhd3eb1b0_0
conda-package-handling 1.9.0 py39h5eee18b_0
conda-repo-cli 1.0.20 py39h06a4308_0
conda-token 0.4.0 pyhd3eb1b0_0
conda-verify 3.4.2 py_1
constantly 15.1.0 pyh2b92418_0
cookiecutter 1.7.3 pyhd3eb1b0_0
cryptography 37.0.1 py39h9ce1e76_0
cssselect 1.1.0 pyhd3eb1b0_0
cuda 11.8.0 0 nvidia
cuda-cccl 11.8.89 0 nvidia
cuda-command-line-tools 11.8.0 0 nvidia
cuda-compiler 11.8.0 0 nvidia
cuda-cudart 11.8.89 0 nvidia
cuda-cudart-dev 11.8.89 0 nvidia
cuda-cuobjdump 11.8.86 0 nvidia
cuda-cupti 11.8.87 0 nvidia
cuda-cuxxfilt 11.8.86 0 nvidia
cuda-demo-suite 11.8.86 0 nvidia
cuda-documentation 11.8.86 0 nvidia
cuda-driver-dev 11.8.89 0 nvidia
cuda-gdb 11.8.86 0 nvidia
cuda-libraries 11.8.0 0 nvidia
cuda-libraries-dev 11.8.0 0 nvidia
cuda-memcheck 11.8.86 0 nvidia
cuda-nsight 11.8.86 0 nvidia
cuda-nsight-compute 11.8.0 0 nvidia
cuda-nvcc 11.8.89 0 nvidia
cuda-nvdisasm 11.8.86 0 nvidia
cuda-nvml-dev 11.8.86 0 nvidia
cuda-nvprof 11.8.87 0 nvidia
cuda-nvprune 11.8.86 0 nvidia
cuda-nvrtc 11.8.89 0 nvidia
cuda-nvrtc-dev 11.8.89 0 nvidia
cuda-nvtx 11.8.86 0 nvidia
cuda-nvvp 11.8.87 0 nvidia
cuda-profiler-api 11.8.86 0 nvidia
cuda-runtime 11.8.0 0 nvidia
cuda-sanitizer-api 11.8.86 0 nvidia
cuda-toolkit 11.8.0 0 nvidia
cuda-tools 11.8.0 0 nvidia
cuda-visual-tools 11.8.0 0 nvidia
curl 7.84.0 h5eee18b_0
cycler 0.11.0 pyhd3eb1b0_0
cython 0.29.32 py39h6a678d5_0
cytoolz 0.11.0 py39h27cfd23_0
daal4py 2021.6.0 py39h79cecc1_1
dal 2021.6.0 hdb19cb5_916
dask 2022.7.0 py39h06a4308_0
dask-core 2022.7.0 py39h06a4308_0
dataclasses 0.8 pyh6d0b6a4_7
datashader 0.14.1 py39h06a4308_0
datashape 0.5.4 py39h06a4308_1
dbus 1.13.18 hb2f20db_0
debugpy 1.5.1 py39h295c915_0
decorator 5.1.1 pyhd3eb1b0_0
defusedxml 0.7.1 pyhd3eb1b0_0
diff-match-patch 20200713 pyhd3eb1b0_0
dill 0.3.4 pyhd3eb1b0_0
distributed 2022.7.0 py39h06a4308_0
docutils 0.18.1 py39h06a4308_3
entrypoints 0.4 py39h06a4308_0
et_xmlfile 1.1.0 py39h06a4308_0
expat 2.4.9 h6a678d5_0
fasteners 0.18 pypi_0 pypi
fftw 3.3.9 h27cfd23_1
filelock 3.6.0 pyhd3eb1b0_0
flake8 4.0.1 pyhd3eb1b0_1
flask 1.1.2 pyhd3eb1b0_0
fontconfig 2.13.1 h6c09931_0
fonttools 4.25.0 pyhd3eb1b0_0
freetype 2.11.0 h70c0345_0
fsspec 2022.7.1 py39h06a4308_0
future 0.18.2 py39h06a4308_1
gds-tools 1.4.0.31 0 nvidia
gensim 4.1.2 py39h295c915_0
giflib 5.2.1 h7b6447c_0
glib 2.69.1 h4ff587b_1
glob2 0.7 pyhd3eb1b0_0
gmp 6.2.1 h295c915_3
gmpy2 2.1.2 py39heeb90bb_0
greenlet 1.1.1 py39h295c915_0
griddataformats 1.0.1 pypi_0 pypi
gsd 2.8.1 pypi_0 pypi
gst-plugins-base 1.14.0 h8213a91_2
gstreamer 1.14.0 h28cd5cc_2
h5py 3.7.0 py39h737f45e_0
hdf5 1.10.6 h3ffc7dd_1
hdf5-1107 1.10.7 0 salilab
heapdict 1.0.1 pyhd3eb1b0_0
holoviews 1.15.0 py39h06a4308_0
hvplot 0.8.0 py39h06a4308_0
hyperlink 21.0.0 pyhd3eb1b0_0
icu 58.2 he6710b0_3
idna 3.3 pyhd3eb1b0_0
imagecodecs 2021.8.26 py39hf0132c2_1
imageio 2.19.3 py39h06a4308_0
imagesize 1.4.1 py39h06a4308_0
importlib-metadata 4.11.3 py39h06a4308_0
importlib_metadata 4.11.3 hd3eb1b0_0
incremental 21.3.0 pyhd3eb1b0_0
inflection 0.5.1 py39h06a4308_0
iniconfig 1.1.1 pyhd3eb1b0_0
intake 0.6.5 pyhd3eb1b0_0
intel-openmp 2021.4.0 h06a4308_3561
intervaltree 3.1.0 pyhd3eb1b0_0
ipykernel 6.15.2 py39h06a4308_0
ipython 7.31.1 py39h06a4308_1
ipython_genutils 0.2.0 pyhd3eb1b0_1
ipywidgets 7.6.5 pyhd3eb1b0_1
isort 5.9.3 pyhd3eb1b0_0
itemadapter 0.3.0 pyhd3eb1b0_0
itemloaders 1.0.4 pyhd3eb1b0_1
itsdangerous 2.0.1 pyhd3eb1b0_0
jdcal 1.4.1 pyhd3eb1b0_0
jedi 0.18.1 py39h06a4308_1
jeepney 0.7.1 pyhd3eb1b0_0
jellyfish 0.9.0 py39h7f8727e_0
jinja2 2.11.3 pyhd3eb1b0_0
jinja2-time 0.2.0 pyhd3eb1b0_3
jmespath 0.10.0 pyhd3eb1b0_0
joblib 1.1.0 pyhd3eb1b0_0
jpeg 9e h7f8727e_0
jq 1.6 h27cfd23_1000
json5 0.9.6 pyhd3eb1b0_0
jsonschema 4.16.0 py39h06a4308_0
jupyter 1.0.0 py39h06a4308_8
jupyter_client 7.3.4 py39h06a4308_0
jupyter_console 6.4.3 pyhd3eb1b0_0
jupyter_core 4.11.1 py39h06a4308_0
jupyter_server 1.18.1 py39h06a4308_0
jupyterlab 3.4.4 py39h06a4308_0
jupyterlab_pygments 0.1.2 py_0
jupyterlab_server 2.10.3 pyhd3eb1b0_1
jupyterlab_widgets 1.0.0 pyhd3eb1b0_1
jxrlib 1.1 h7b6447c_2
keyring 23.4.0 py39h06a4308_0
kiwisolver 1.4.2 py39h295c915_0
krb5 1.19.2 hac12032_0
lazy-object-proxy 1.6.0 py39h27cfd23_0
lcms2 2.12 h3be6417_0
ld_impl_linux-64 2.38 h1181459_1
lerc 3.0 h295c915_0
libaec 1.0.4 he6710b0_1
libarchive 3.6.1 hab531cd_0
libbrotlicommon 1.0.9 h5eee18b_7
libbrotlidec 1.0.9 h5eee18b_7
libbrotlienc 1.0.9 h5eee18b_7
libclang 10.0.1 default_hb85057a_2
libcublas 11.11.3.6 0 nvidia
libcublas-dev 11.11.3.6 0 nvidia
libcufft 10.9.0.58 0 nvidia
libcufft-dev 10.9.0.58 0 nvidia
libcufile 1.4.0.31 0 nvidia
libcufile-dev 1.4.0.31 0 nvidia
libcurand 10.3.0.86 0 nvidia
libcurand-dev 10.3.0.86 0 nvidia
libcurl 7.84.0 h91b91d3_0
libcusolver 11.4.1.48 0 nvidia
libcusolver-dev 11.4.1.48 0 nvidia
libcusparse 11.7.5.86 0 nvidia
libcusparse-dev 11.7.5.86 0 nvidia
libdeflate 1.8 h7f8727e_5
libedit 3.1.20210910 h7f8727e_0
libev 4.33 h7f8727e_1
libevent 2.1.12 h8f2d780_0
libffi 3.3 he6710b0_2
libgcc-ng 11.2.0 h1234567_1
libgfortran-ng 11.2.0 h00389a5_1
libgfortran5 11.2.0 h1234567_1
libgomp 11.2.0 h1234567_1
libidn2 2.3.2 h7f8727e_0
liblief 0.11.5 h295c915_1
libllvm10 10.0.1 hbcb73fb_5
libllvm11 11.1.0 h9e868ea_5
libnghttp2 1.46.0 hce63b2e_0
libnpp 11.8.0.86 0 nvidia
libnpp-dev 11.8.0.86 0 nvidia
libnvjpeg 11.9.0.86 0 nvidia
libnvjpeg-dev 11.9.0.86 0 nvidia
libpng 1.6.37 hbc83047_0
libpq 12.9 h16c4e8d_3
libsodium 1.0.18 h7b6447c_0
libspatialindex 1.9.3 h2531618_0
libssh2 1.10.0 h8f2d780_0
libstdcxx-ng 11.2.0 h1234567_1
libtiff 4.4.0 hecacb30_0
libunistring 0.9.10 h27cfd23_0
libuuid 1.0.3 h7f8727e_2
libwebp 1.2.2 h55f646e_0
libwebp-base 1.2.2 h7f8727e_0
libxcb 1.15 h7f8727e_0
libxkbcommon 1.0.1 hfa300c1_0
libxml2 2.9.14 h74e7548_0
libxslt 1.1.35 h4e12654_0
libzopfli 1.0.3 he6710b0_0
llvmlite 0.38.0 py39h4ff587b_0
locket 1.0.0 py39h06a4308_0
lxml 4.9.1 py39h1edc446_0
lz4 3.1.3 py39h27cfd23_0
lz4-c 1.9.3 h295c915_1
lzo 2.10 h7b6447c_2
markdown 3.3.4 py39h06a4308_0
markupsafe 2.0.1 py39h27cfd23_0
matplotlib 3.5.2 py39h06a4308_0
matplotlib-base 3.5.2 py39hf590b9c_0
matplotlib-inline 0.1.6 py39h06a4308_0
mccabe 0.7.0 pyhd3eb1b0_0
mdanalysis 2.4.3 pypi_0 pypi
mistune 0.8.4 py39h27cfd23_1000
mkl 2021.4.0 h06a4308_640
mkl-service 2.4.0 py39h7f8727e_0
mkl_fft 1.3.1 py39hd3c417c_0
mkl_random 1.2.2 py39h51133e4_0
mmtf-python 1.1.3 pypi_0 pypi
mock 4.0.3 pyhd3eb1b0_0
modeller 10.4 py39h9bf148f_0 salilab
mpc 1.1.0 h10f8cd9_1
mpfr 4.0.2 hb69a4c5_1
mpi 1.0 mpich
mpich 3.3.2 external_0
mpmath 1.2.1 py39h06a4308_0
mrcfile 1.4.3 pypi_0 pypi
msgpack-python 1.0.3 py39hd09550d_0
multipledispatch 0.6.0 py39h06a4308_0
munkres 1.1.4 py_0
mypy_extensions 0.4.3 py39h06a4308_1
navigator-updater 0.3.0 py39h06a4308_0
nbclassic 0.3.5 pyhd3eb1b0_0
nbclient 0.5.13 py39h06a4308_0
nbconvert 6.4.4 py39h06a4308_0
nbformat 5.5.0 py39h06a4308_0
ncurses 6.3 h5eee18b_3
nest-asyncio 1.5.5 py39h06a4308_0
networkx 2.8.4 py39h06a4308_0
nltk 3.7 pyhd3eb1b0_0
nose 1.3.7 pyhd3eb1b0_1008
notebook 6.4.12 py39h06a4308_0
nsight-compute 2022.3.0.22 0 nvidia
nspr 4.33 h295c915_0
nss 3.74 h0370c37_0
numba 0.55.1 py39h51133e4_0
numexpr 2.8.3 py39h807cd23_0
numpy 1.21.5 py39h6c91a56_3
numpy-base 1.21.5 py39ha15fc14_3
numpydoc 1.4.0 py39h06a4308_0
olefile 0.46 pyhd3eb1b0_0
oniguruma 6.9.7.1 h27cfd23_0
openbabel 3.1.1 py39hee2736e_2 conda-forge
openjpeg 2.4.0 h3ad879b_0
openpyxl 3.0.10 py39h5eee18b_0
openssl 1.1.1q h7f8727e_0
packaging 21.3 pyhd3eb1b0_0
pandas 1.4.4 py39h6a678d5_0
pandocfilters 1.5.0 pyhd3eb1b0_0
panel 0.13.1 py39h06a4308_0
param 1.12.0 pyhd3eb1b0_0
parsel 1.6.0 py39h06a4308_0
parso 0.8.3 pyhd3eb1b0_0
partd 1.2.0 pyhd3eb1b0_1
patch 2.7.6 h7b6447c_1001
patchelf 0.13 h295c915_0
pathlib 1.0.1 pyhd3eb1b0_1
pathspec 0.9.0 py39h06a4308_0
patsy 0.5.2 py39h06a4308_1
pcre 8.45 h295c915_0
pep8 1.7.1 py39h06a4308_1
pexpect 4.8.0 pyhd3eb1b0_3
pickleshare 0.7.5 pyhd3eb1b0_1003
pillow 9.2.0 py39hace64e9_1
pip 22.2.2 py39h06a4308_0
pixman 0.40.0 h36c2ea0_0 conda-forge
pkginfo 1.8.2 pyhd3eb1b0_0
platformdirs 2.5.2 py39h06a4308_0
plotly 5.9.0 py39h06a4308_0
pluggy 1.0.0 py39h06a4308_1
ply 3.11 py39h06a4308_0
poyo 0.5.0 pyhd3eb1b0_0
prometheus_client 0.14.1 py39h06a4308_0
prompt-toolkit 3.0.20 pyhd3eb1b0_0
prompt_toolkit 3.0.20 hd3eb1b0_0
protego 0.1.16 py_0
psutil 5.9.0 py39h5eee18b_0
ptyprocess 0.7.0 pyhd3eb1b0_2
py 1.11.0 pyhd3eb1b0_0
py-lief 0.11.5 py39h295c915_1
pyasn1 0.4.8 pyhd3eb1b0_0
pyasn1-modules 0.2.8 py_0
pycodestyle 2.8.0 pyhd3eb1b0_0
pycosat 0.6.3 py39h27cfd23_0
pycparser 2.21 pyhd3eb1b0_0
pyct 0.4.8 py39h06a4308_1
pycurl 7.45.1 py39h8f2d780_0
pydispatcher 2.0.5 py39h06a4308_2
pydocstyle 6.1.1 pyhd3eb1b0_0
pyerfa 2.0.0 py39h27cfd23_0
pyflakes 2.4.0 pyhd3eb1b0_0
pygments 2.11.2 pyhd3eb1b0_0
pyhamcrest 2.0.2 pyhd3eb1b0_2
pyjwt 2.4.0 py39h06a4308_0
pylint 2.14.5 py39h06a4308_0
pyls-spyder 0.4.0 pyhd3eb1b0_0
pyodbc 4.0.34 py39h6a678d5_0
pyopenssl 22.0.0 pyhd3eb1b0_0
pyparsing 3.0.9 py39h06a4308_0
pyqt 5.15.7 py39h6a678d5_1
pyqt5-sip 12.11.0 py39h6a678d5_1
pyqtwebengine 5.15.7 py39h6a678d5_1
pyrsistent 0.18.0 py39heee7806_0
pysocks 1.7.1 py39h06a4308_0
pytables 3.6.1 py39h77479fe_1
pytest 7.1.2 py39h06a4308_0
python 3.9.13 haa1d7c7_1
python-dateutil 2.8.2 pyhd3eb1b0_0
python-fastjsonschema 2.16.2 py39h06a4308_0
python-libarchive-c 2.9 pyhd3eb1b0_1
python-lsp-black 1.2.1 py39h06a4308_0
python-lsp-jsonrpc 1.0.0 pyhd3eb1b0_0
python-lsp-server 1.5.0 py39h06a4308_0
python-slugify 5.0.2 pyhd3eb1b0_0
python-snappy 0.6.0 py39h2531618_3
python_abi 3.9 2_cp39 conda-forge
pytz 2022.1 py39h06a4308_0
pyviz_comms 2.0.2 pyhd3eb1b0_0
pywavelets 1.3.0 py39h7f8727e_0
pyxdg 0.27 pyhd3eb1b0_0
pyyaml 6.0 py39h7f8727e_1
pyzmq 23.2.0 py39h6a678d5_0
qdarkstyle 3.0.2 pyhd3eb1b0_0
qstylizer 0.1.10 pyhd3eb1b0_0
qt 5.15.9 h06a4308_0
qt-main 5.15.2 h327a75a_7
qt-webengine 5.15.9 hd2b0992_4
qtawesome 1.0.3 pyhd3eb1b0_0
qtconsole 5.3.2 py39h06a4308_0
qtpy 2.2.0 py39h06a4308_0
qtwebkit 5.212 h4eab89a_4
queuelib 1.5.0 py39h06a4308_0
readline 8.1.2 h7f8727e_1
regex 2022.7.9 py39h5eee18b_0
requests 2.28.1 py39h06a4308_0
requests-file 1.5.1 pyhd3eb1b0_0
ripgrep 13.0.0 hbdeaff8_0
rope 0.22.0 pyhd3eb1b0_0
rtree 0.9.7 py39h06a4308_1
ruamel_yaml 0.15.100 py39h27cfd23_0
s3transfer 0.6.0 py39h06a4308_0
scikit-image 0.19.2 py39h51133e4_0
scikit-learn 1.0.2 py39h51133e4_1
scikit-learn-intelex 2021.6.0 py39h06a4308_0
scipy 1.9.1 py39h14f4228_0
scrapy 2.6.2 py39h06a4308_0
seaborn 0.11.2 pyhd3eb1b0_0
secretstorage 3.3.1 py39h06a4308_0
send2trash 1.8.0 pyhd3eb1b0_1
service_identity 18.1.0 pyhd3eb1b0_1
setuptools 63.4.1 py39h06a4308_0
sip 6.6.2 py39h6a678d5_0
six 1.16.0 pyhd3eb1b0_1
smart_open 5.2.1 py39h06a4308_0
snappy 1.1.9 h295c915_0
sniffio 1.2.0 py39h06a4308_1
snowballstemmer 2.2.0 pyhd3eb1b0_0
sortedcollections 2.1.0 pyhd3eb1b0_0
sortedcontainers 2.4.0 pyhd3eb1b0_0
soupsieve 2.3.1 pyhd3eb1b0_0
sphinx 5.0.2 py39h06a4308_0
sphinxcontrib-applehelp 1.0.2 pyhd3eb1b0_0
sphinxcontrib-devhelp 1.0.2 pyhd3eb1b0_0
sphinxcontrib-htmlhelp 2.0.0 pyhd3eb1b0_0
sphinxcontrib-jsmath 1.0.1 pyhd3eb1b0_0
sphinxcontrib-qthelp 1.0.3 pyhd3eb1b0_0
sphinxcontrib-serializinghtml 1.1.5 pyhd3eb1b0_0
spyder 5.3.3 py39h06a4308_0
spyder-kernels 2.3.3 py39h06a4308_0
sqlalchemy 1.4.39 py39h5eee18b_0
sqlite 3.39.3 h5082296_0
statsmodels 0.13.2 py39h7f8727e_0
sympy 1.10.1 py39h06a4308_0
tabulate 0.8.10 py39h06a4308_0
tbb 2021.6.0 hdb19cb5_0
tbb4py 2021.6.0 py39hdb19cb5_0
tblib 1.7.0 pyhd3eb1b0_0
tenacity 8.0.1 py39h06a4308_1
terminado 0.13.1 py39h06a4308_0
testpath 0.6.0 py39h06a4308_0
text-unidecode 1.3 pyhd3eb1b0_0
textdistance 4.2.1 pyhd3eb1b0_0
threadpoolctl 2.2.0 pyh0d69192_0
three-merge 0.1.1 pyhd3eb1b0_0
tifffile 2021.7.2 pyhd3eb1b0_2
tinycss 0.4 pyhd3eb1b0_1002
tk 8.6.12 h1ccaba5_0
tldextract 3.2.0 pyhd3eb1b0_0
toml 0.10.2 pyhd3eb1b0_0
tomli 2.0.1 py39h06a4308_0
tomlkit 0.11.1 py39h06a4308_0
toolz 0.11.2 pyhd3eb1b0_0
tornado 6.1 py39h27cfd23_0
tqdm 4.64.1 py39h06a4308_0
traitlets 5.1.1 pyhd3eb1b0_0
twisted 22.2.0 py39h5eee18b_1
typing-extensions 4.3.0 py39h06a4308_0
typing_extensions 4.3.0 py39h06a4308_0
tzdata 2022c h04d1e81_0
ujson 5.4.0 py39h6a678d5_0
unidecode 1.2.0 pyhd3eb1b0_0
unixodbc 2.3.11 h5eee18b_0
urllib3 1.26.11 py39h06a4308_0
w3lib 1.21.0 pyhd3eb1b0_0
watchdog 2.1.6 py39h06a4308_0
wcwidth 0.2.5 pyhd3eb1b0_0
webencodings 0.5.1 py39h06a4308_1
websocket-client 0.58.0 py39h06a4308_4
werkzeug 2.0.3 pyhd3eb1b0_0
wget 1.21.3 h0b77cf5_0
whatthepatch 1.0.2 py39h06a4308_0
wheel 0.37.1 pyhd3eb1b0_0
widgetsnbextension 3.5.2 py39h06a4308_0
wrapt 1.14.1 py39h5eee18b_0
wurlitzer 3.0.2 py39h06a4308_0
xarray 0.20.1 pyhd3eb1b0_1
xlrd 2.0.1 pyhd3eb1b0_0
xlsxwriter 3.0.3 pyhd3eb1b0_0
xz 5.2.6 h5eee18b_0
yaml 0.2.5 h7b6447c_0
yapf 0.31.0 pyhd3eb1b0_0
zeromq 4.3.4 h2531618_0
zfp 0.5.5 h295c915_6
zict 2.1.0 py39h06a4308_0
zipp 3.8.0 py39h06a4308_0
zlib 1.2.12 h5eee18b_3
zope 1.0 py39h06a4308_1
zope.interface 5.4.0 py39h7f8727e_0
zstd 1.5.2 ha4553b6_0
(base)
Mario Sergio Valdes
May 15, 2023, 4:22:36 PM5/15/23
to gmx_MMPBSA
This is the (base) environment. Please, activate the gmxMMPBSA environment and execute conda list again
Faizul Azam
May 16, 2023, 5:15:03 PM5/16/23
to gmx_MMPBSA
Thank you. Here is the list:
(gmxMMPBSA) conda list
# packages in environment at /home/drazzam/anaconda3/envs/gmxMMPBSA:#
# Name Version Build Channel
_openmp_mutex 4.5 2_gnu conda-forge
ambertools 21.12 py39hc630cb1_0 conda-forge
amberutils 21.0 pypi_0 pypi
arpack 3.7.0 hdefa2d7_2 conda-forge
binutils 2.39 hdd6e379_1 conda-forge
binutils_impl_linux-64 2.39 he00db2b_1 conda-forge
binutils_linux-64 2.39 h5fc0e48_13 conda-forge
boost-cpp 1.74.0 h75c5d50_8 conda-forge
brotli 1.0.9 h166bdaf_8 conda-forge
brotli-bin 1.0.9 h166bdaf_8 conda-forge
brotlipy 0.7.0 py39hb9d737c_1005 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
c-compiler 1.2.0 h7f98852_0 conda-forge
ca-certificates 2023.5.7 hbcca054_0 conda-forge
certifi 2023.5.7 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py39he91dace_3 conda-forge
charset-normalizer 3.1.0 pyhd8ed1ab_0 conda-forge
compilers 1.2.0 ha770c72_0 conda-forge
contourpy 1.0.7 py39h4b4f3f3_0 conda-forge
cryptography 39.0.0 py39hd598818_0 conda-forge
curl 7.87.0 h6312ad2_0 conda-forge
cxx-compiler 1.2.0 h4bd325d_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cython 0.29.34 py39h227be39_0 conda-forge
expat 2.5.0 hcb278e6_1 conda-forge
fftw 3.3.10 nompi_hc118613_107 conda-forge
fonttools 4.39.4 py39hd1e30aa_0 conda-forge
fortran-compiler 1.2.0 h1990efc_0 conda-forge
freetype 2.12.1 hca18f0e_1 conda-forge
gcc_impl_linux-64 9.5.0 h99780fb_19 conda-forge
gcc_linux-64 9.5.0 h4258300_13 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
gfortran_impl_linux-64 9.5.0 hf1096a2_19 conda-forge
gfortran_linux-64 9.5.0 hdb51d14_13 conda-forge
git 2.39.1 pl5321ha3eba64_0 conda-forge
gmx-mmpbsa 1.6.1 pypi_0 pypi
gromacs 2022.4 nompi_hca75aac_100 conda-forge
gxx_impl_linux-64 9.5.0 h99780fb_19 conda-forge
gxx_linux-64 9.5.0 h43f449f_13 conda-forge
hdf4 4.2.15 h9772cbc_5 conda-forge
hdf5 1.12.2 nompi_h2386368_101 conda-forge
icu 70.1 h27087fc_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
importlib-resources 5.12.0 pyhd8ed1ab_0 conda-forge
importlib_resources 5.12.0 pyhd8ed1ab_0 conda-forge
jpeg 9e h0b41bf4_3 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.4 py39hf939315_1 conda-forge
krb5 1.20.1 hf9c8cef_0 conda-forge
lcms2 2.15 hfd0df8a_0 conda-forge
ld_impl_linux-64 2.39 hcc3a1bd_1 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libaec 1.0.6 hcb278e6_1 conda-forge
libblas 3.9.0 16_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_8 conda-forge
libbrotlidec 1.0.9 h166bdaf_8 conda-forge
libbrotlienc 1.0.9 h166bdaf_8 conda-forge
libcblas 3.9.0 16_linux64_openblas conda-forge
libcurl 7.87.0 h6312ad2_0 conda-forge
libdeflate 1.17 h0b41bf4_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-devel_linux-64 9.5.0 h0a57e50_19 conda-forge
libgcc-ng 12.2.0 h65d4601_19 conda-forge
libgfortran-ng 12.2.0 h69a702a_19 conda-forge
libgfortran5 12.2.0 h337968e_19 conda-forge
libgomp 12.2.0 h65d4601_19 conda-forge
libhwloc 2.9.0 hd6dc26d_0 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
liblapack 3.9.0 16_linux64_openblas conda-forge
libnetcdf 4.8.1 nompi_h261ec11_106 conda-forge
libnghttp2 1.51.0 hdcd2b5c_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
libsanitizer 9.5.0 h2f262e1_19 conda-forge
libsqlite 3.41.2 h2797004_1 conda-forge
libssh2 1.10.0 haa6b8db_3 conda-forge
libstdcxx-devel_linux-64 9.5.0 h0a57e50_19 conda-forge
libstdcxx-ng 12.2.0 h46fd767_19 conda-forge
libtiff 4.5.0 h6adf6a1_2 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.3.0 h0b41bf4_0 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxml2 2.10.3 hca2bb57_4 conda-forge
libzip 1.9.2 hc869a4a_1 conda-forge
libzlib 1.2.13 h166bdaf_4 conda-forge
matplotlib-base 3.7.1 py39he190548_0 conda-forge
mpi 1.0 mpich conda-forge
mpi4py 3.1.3 py39h32b9844_3 conda-forge
mpich 4.1.1 h846660c_100 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
netcdf-fortran 4.5.4 nompi_hc402ea5_102 conda-forge
numpy 1.24.3 py39h6183b62_0 conda-forge
ocl-icd 2.3.1 h7f98852_0 conda-forge
ocl-icd-system 1.0.0 1 conda-forge
openjpeg 2.5.0 hfec8fc6_2 conda-forge
openssl 1.1.1t h0b41bf4_0 conda-forge
packaging 23.1 pyhd8ed1ab_0 conda-forge
packmol 20.010 h86c2bf4_0 conda-forge
packmol-memgen 1.2.1rc0 pypi_0 pypi
pandas 1.2.2 pypi_0 pypi
parmed 3.4.3+11.g41cc9ab pypi_0 pypi
pcre2 10.40 hc3806b6_0 conda-forge
perl 5.32.1 2_h7f98852_perl5 conda-forge
pillow 9.4.0 py39h2320bf1_1 conda-forge
pip 23.1.2 pyhd8ed1ab_0 conda-forge
platformdirs 3.5.1 pyhd8ed1ab_0 conda-forge
pooch 1.7.0 pyha770c72_3 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyopenssl 23.1.1 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge
pyqt5 5.15.6 pypi_0 pypi
pyqt5-qt5 5.15.2 pypi_0 pypi
pyqt5-sip 12.12.1 pypi_0 pypi
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.9.15 h47a2c10_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge
python_abi 3.9 3_cp39 conda-forge
pytraj 2.0.6 pypi_0 pypi
pytz 2023.3 pyhd8ed1ab_0 conda-forge
readline 8.2 h8228510_1 conda-forge
requests 2.29.0 pyhd8ed1ab_0 conda-forge
sander 16.0 pypi_0 pypi
scipy 1.10.1 py39h6183b62_3 conda-forge
seaborn 0.11.2 pypi_0 pypi
setuptools 67.7.2 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sysroot_linux-64 2.12 he073ed8_15 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tqdm 4.65.0 pypi_0 pypi
typing-extensions 4.5.0 hd8ed1ab_0 conda-forge
typing_extensions 4.5.0 pyha770c72_0 conda-forge
tzdata 2023c h71feb2d_0 conda-forge
unicodedata2 15.0.0 py39hb9d737c_0 conda-forge
urllib3 1.26.15 pyhd8ed1ab_0 conda-forge
wheel 0.40.0 pyhd8ed1ab_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.8.4 h0b41bf4_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxt 1.2.1 h7f98852_2 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zipp 3.15.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 h166bdaf_4 conda-forge
zstd 1.5.2 h3eb15da_6 conda-forge
(gmxMMPBSA)
Mario Sergio Valdes
May 16, 2023, 10:19:42 PM5/16/23
to gmx_MMPBSA
You have all the dependencies, but for some reason, it's not working correctly... Please, run it serially and attach the gmx_MMPBSA.log file
Faizul Azam
May 22, 2023, 3:18:31 PM5/22/23
to gmx_MMPBSA
Hi Mario
Here is the log file and terminal events:
(base) conda activate gmx_MMPBSA
EnvironmentNameNotFound: Could not find conda environment: gmx_MMPBSA
You can list all discoverable environments with `conda info --envs`.
(base) conda activate gmxMMPBSA
(gmxMMPBSA) gmx_MMPBSA -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
gmx_MMPBSA -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
tets
EnvironmentNameNotFound: Could not find conda environment: gmx_MMPBSA
You can list all discoverable environments with `conda info --envs`.
(base) conda activate gmxMMPBSA
(gmxMMPBSA) gmx_MMPBSA -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
gmx_MMPBSA -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
tets
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
(gmxMMPBSA) mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md-nowat.tpr -ct md-wh-nj-fit.xtc -ci index2.ndx -cg 1 13 -cp trp.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui -lm Ligand_user_gaff2.mol2
tets
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/drazzam/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[57898,1],0]
Exit code: 1
--------------------------------------------------------------------------
(gmxMMPBSA)
Mario Sergio Valdes
May 22, 2023, 3:32:06 PM5/22/23
to gmx_MMPBSA
As you can see in the gmx_MMPBSA.log file, you are using the system mpirun (
/opt/openmpi411/bin/mpirun). So, this is an incompatibility problem. Please try to use the conda mpi
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