INFO ] Running calculations on normal system...
[INFO ] Beginning PB calculations with /home/bif-sssihl-12/miniconda3/envs/AmberTools23/bin/sander
[INFO ] calculating complex contribution...
100%|#################################################################################################################################################| 100/100 [elapsed: 33:40 remaining: 00:00]
[INFO ] calculating receptor contribution...
100%|#################################################################################################################################################| 100/100 [elapsed: 33:34 remaining: 00:00]
[INFO ] calculating ligand contribution...
100%|#################################################################################################################################################| 100/100 [elapsed: 00:53 remaining: 00:00]
[INFO ] Parsing results to output files...
[ERROR ] MMPBSA_Error
Some energy terms are undefined. Please, check the input structure and trajectory. Check this section the docs for more info
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/Q%26A/calculations/#possible-solutionsCheck the gmx_MMPBSA.log file to report the problem.
File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 109, in gmxmmpbsa
app.parse_output_files()
File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1206, in parse_output_files
self.calc_types.normal[key]['complex'].parse_from_file(self.pre + basename[i] % 'complex',
File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 108, in parse_from_file
AmberOutput._read(self)
File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 197, in _read
self._get_energies(output_file)
File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 740, in _get_energies
self['BOND'][self.frame_idx] = conv_float(words[2])
File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 603, in conv_float
GMXMMPBSA_ERROR('Some energy terms are undefined. Please, check the input structure and trajectory. Check this '
File "/home/bif-sssihl-12/miniconda3/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:
Some energy terms are undefined. Please, check the input structure and trajectory. Check this section the docs for more info
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/Q%26A/calculations/#possible-solutionsCheck the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.