فاطمه بیانی
Dec 22, 2021, 1:33:35 PM12/22/21
to gmx_m...@googlegroups.com
,Hello gmx-mmpbsa users
I have Protein-Ligand comlexe, these complexe undergo simmulution by GROMACS. I got this error to calculate gmx-mmpbsa
(AmberTools21) yahya@yahya:/media/yahya/HP V245L/NEone-WIILD/mmpbsa$ mpirun -np 2 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md_protein.tpr -ci index-mini.ndx -cg 1 13 -ct md_protein.xtc -cp topol.top
[INFO ] Starting
[INFO ] Command-line
gmx_MMPBSA -O -i mmpbsa.in -cs md_protein.tpr -ci index-mini.ndx -cg 1 13 -ct md_protein.xtc -cp topol.top
[WARNING] protein_forcefield and ligand_forcefield variables are deprecate since version 1.4.1 and will be remove in the next version. Please, use forcefield instead.
[WARNING] entropy_seg variable is deprecate since version 1.4.2 and will be remove in v1.5.0. Please, use ie_segment instead.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/yahya/Downloads/yes/envs/AmberTools21/bin/cpptraj
[INFO ] tleap found! Using /home/yahya/Downloads/yes/envs/AmberTools21/bin/tleap
[INFO ] parmchk2 found! Using /home/yahya/Downloads/yes/envs/AmberTools21/bin/parmchk2
[INFO ] sander found! Using /home/yahya/Downloads/yes/envs/AmberTools21/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /usr/bin/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER Topologies from GROMACS files...
[INFO ] Checking gmxMMPBSA data folder exists in Amber data...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Normal Complex: Saving group 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 Complex: Saving group 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 13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Building Normal Complex Amber Topology...
File "/home/yahya/Downloads/yes/envs/AmberTools21/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 95, in gmxmmpbsa
app.make_prmtops()
File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 576, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 117, in buildTopology
tops = self.gmxtop2prmtop()
File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 318, in gmxtop2prmtop
com_top = self.cleantop(self.FILES.complex_top, self.indexes[0] + self.indexes[1])
File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 598, in cleantop
rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
self.read(fname, defines, parametrize)
File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 366, in read
b, bt = self._parse_vsites3(line, molecule.atoms, params)
File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 683, in _parse_vsites3
raise GromacsError('Only 3-point vsite type 1 is supported')
GromacsError: Only 3-point vsite type 1 is supported
Error occured on rank 0.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[INFO ] Starting
[INFO ] Command-line
gmx_MMPBSA -O -i mmpbsa.in -cs md_protein.tpr -ci index-mini.ndx -cg 1 13 -ct md_protein.xtc -cp topol.top
[WARNING] protein_forcefield and ligand_forcefield variables are deprecate since version 1.4.1 and will be remove in the next version. Please, use forcefield instead.
[WARNING] entropy_seg variable is deprecate since version 1.4.2 and will be remove in v1.5.0. Please, use ie_segment instead.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/yahya/Downloads/yes/envs/AmberTools21/bin/cpptraj
[INFO ] tleap found! Using /home/yahya/Downloads/yes/envs/AmberTools21/bin/tleap
[INFO ] parmchk2 found! Using /home/yahya/Downloads/yes/envs/AmberTools21/bin/parmchk2
[INFO ] sander found! Using /home/yahya/Downloads/yes/envs/AmberTools21/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /usr/bin/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER Topologies from GROMACS files...
[INFO ] Checking gmxMMPBSA data folder exists in Amber data...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Normal Complex: Saving group 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 Complex: Saving group 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 13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Building Normal Complex Amber Topology...
File "/home/yahya/Downloads/yes/envs/AmberTools21/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 95, in gmxmmpbsa
app.make_prmtops()
File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 576, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 117, in buildTopology
tops = self.gmxtop2prmtop()
File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 318, in gmxtop2prmtop
com_top = self.cleantop(self.FILES.complex_top, self.indexes[0] + self.indexes[1])
File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 598, in cleantop
rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
self.read(fname, defines, parametrize)
File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 366, in read
b, bt = self._parse_vsites3(line, molecule.atoms, params)
File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 683, in _parse_vsites3
raise GromacsError('Only 3-point vsite type 1 is supported')
GromacsError: Only 3-point vsite type 1 is supported
Error occured on rank 0.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Kindly help me, please.
Thank you.
marioe911116
Dec 22, 2021, 1:48:14 PM12/22/21
to gmx_MMPBSA
Hello there! I see you used charmm-gui to generate your files... is that correct? the fastest way to deal with these kinds of errors is by sending us the files you are using (*.in, *.tpr, *.ndx, *.top with all the folders and files associated and a small piece of the trajectory -- 5 frames is enough)
cheers!
Mario E.
فاطمه بیانی
Dec 22, 2021, 3:15:32 PM12/22/21
to gmx_MMPBSA
Yes i used charmm-gui to generate files.
were the files received?
thank you
thank you
marioe911116 در تاریخ چهارشنبه ۲۲ دسامبر ۲۰۲۱ ساعت ۲۲:۱۸:۱۴ (UTC+3:30) نوشت:
marioe911116
Dec 22, 2021, 3:27:14 PM12/22/21
to gmx_MMPBSA
Yes, I did receive the files. I found the problem and is that the ligand contains LP particles with are not supported in gmx_MMPBSA... you can follow this tutorial to work around this problem...
cheers!
Mario E.
فاطمه بیانی
Dec 22, 2021, 3:31:47 PM12/22/21
to gmx_MMPBSA
Thank you very much dear
marioe911116 در تاریخ چهارشنبه ۲۲ دسامبر ۲۰۲۱ ساعت ۲۳:۵۷:۱۴ (UTC+3:30) نوشت:
negin s
Dec 23, 2021, 2:37:10 PM12/23/21
to gmx_m...@googlegroups.com
Hello gmx_mmpbsa users, I did S1-ACE2_complex_7dmu example of gmx-mmpbsa but I got the following error :
(AmberTools21) safaei@ubuntu:~/Downloads/gmx_MMPBSA-master/docs/examples/COVID-19_related_proteins/S1-ACE2_complex_7dmu$ gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 20 19 -ct com_traj.xtc -cp topol.top
[INFO ] Starting
[INFO ] Command-line
gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 20 19 -ct com_traj.xtc -cp topol.top
[INFO ] Starting
[INFO ] Command-line
gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 20 19 -ct com_traj.xtc -cp topol.top
[WARNING] protein_forcefield and ligand_forcefield variables are deprecate since version 1.4.1 and will be remove in the next version. Please, use forcefield instead.
[WARNING] entropy_seg variable is deprecate since version 1.4.2 and will be remove in v1.5.0. Please, use ie_segment instead.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/safaei/anaconda3/envs/AmberTools21/bin/cpptraj
[INFO ] tleap found! Using /home/safaei/anaconda3/envs/AmberTools21/bin/tleap
[INFO ] parmchk2 found! Using /home/safaei/anaconda3/envs/AmberTools21/bin/parmchk2
[INFO ] sander found! Using /home/safaei/anaconda3/envs/AmberTools21/bin/sander
[INFO ] tleap found! Using /home/safaei/anaconda3/envs/AmberTools21/bin/tleap
[INFO ] parmchk2 found! Using /home/safaei/anaconda3/envs/AmberTools21/bin/parmchk2
[INFO ] sander found! Using /home/safaei/anaconda3/envs/AmberTools21/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /usr/local/gromacs/bin/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER Topologies from GROMACS files...
[INFO ] Checking gmxMMPBSA data folder exists in Amber data...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Normal Complex: Saving group 20_19 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 Complex: Saving group 20 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 19 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Building Normal Complex Amber Topology...
[INFO ] Writing Normal Complex Amber Topology...
[INFO ] No Receptor topology files was defined. Using ST approach...
[INFO ] Building AMBER Receptor Topology from Complex...
[INFO ] No Ligand Topology files was defined. Using ST approach...
[INFO ] Building AMBER Ligand Topology from Complex...
[INFO ] Cleaning normal complex trajectories...
[INFO ] Building AMBER Topologies from GROMACS files...Done.
[INFO ] Loading and checking parameter files for compatibility...
CHAMBER prmtops found. Forcing use of sander
Preparing trajectories for simulation...
6 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /home/safaei/anaconda3/envs/AmberTools21/bin/sander
calculating complex contribution...
[ERROR ] CalcError /home/safaei/anaconda3/envs/AmberTools21/bin/sander failed with prmtop COM.prmtop!
If you are using sander and PB calculation, check the *.mdout files to get the sander error and check this thread (http://archive.ambermd.org/201303/0548.html)
.
Check the gmx_MMPBSA.log file to report the problem.
File "/home/safaei/anaconda3/envs/AmberTools21/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.run_mmpbsa()
File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 209, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 84, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 433, in run
GMXMMPBSA_ERROR('%s failed with prmtop %s!\n\t' % (self.program, self.prmtop) +
File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in __init__
raise exc(msg + '. Check the gmx_MMPBSA.log file to report the problem.')
CalcError: /home/safaei/anaconda3/envs/AmberTools21/bin/sander failed with prmtop COM.prmtop!
If you are using sander and PB calculation, check the *.mdout files to get the sander error and check this thread (http://archive.ambermd.org/201303/0548.html)
. Check the gmx_MMPBSA.log file to report the problem.
[INFO ] No Receptor topology files was defined. Using ST approach...
[INFO ] Building AMBER Receptor Topology from Complex...
[INFO ] No Ligand Topology files was defined. Using ST approach...
[INFO ] Building AMBER Ligand Topology from Complex...
[INFO ] Cleaning normal complex trajectories...
[INFO ] Building AMBER Topologies from GROMACS files...Done.
[INFO ] Loading and checking parameter files for compatibility...
CHAMBER prmtops found. Forcing use of sander
Preparing trajectories for simulation...
6 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /home/safaei/anaconda3/envs/AmberTools21/bin/sander
calculating complex contribution...
[ERROR ] CalcError /home/safaei/anaconda3/envs/AmberTools21/bin/sander failed with prmtop COM.prmtop!
If you are using sander and PB calculation, check the *.mdout files to get the sander error and check this thread (http://archive.ambermd.org/201303/0548.html)
.
Check the gmx_MMPBSA.log file to report the problem.
File "/home/safaei/anaconda3/envs/AmberTools21/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.run_mmpbsa()
File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 209, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 84, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 433, in run
GMXMMPBSA_ERROR('%s failed with prmtop %s!\n\t' % (self.program, self.prmtop) +
File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in __init__
raise exc(msg + '. Check the gmx_MMPBSA.log file to report the problem.')
CalcError: /home/safaei/anaconda3/envs/AmberTools21/bin/sander failed with prmtop COM.prmtop!
If you are using sander and PB calculation, check the *.mdout files to get the sander error and check this thread (http://archive.ambermd.org/201303/0548.html)
. Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
Kindly help me
Thank you
marioe911116
Dec 23, 2021, 2:43:11 PM12/23/21
to gmx_MMPBSA
could you please sned one of the *.mdout files?
Mario Ernesto
Dec 26, 2021, 6:46:14 PM12/26/21
to فاطمه بیانی, gmx_MMPBSA
Seems like you have a carbohydrate in your system... If that is the case, follow this tutorial
Or simply include the topology flag in the command line:
gmx_MMPBSA -O -i mmpbsa.in -cs md_protein.tpr -ci index2.ndx -cg 23 25 -ct md_protein.xtc -cp topol.top
--
You received this message because you are subscribed to the Google Groups "gmx_MMPBSA" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gmx_mmpbsa+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/CACOn43MPWu6H6CRoUsDZqMjr3thTWDuA3pGZGu-6kNHdiUMPAg%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.
Message has been deleted
فاطمه بیانی
Dec 26, 2021, 6:56:30 PM12/26/21
to gmx_MMPBSA
Thanks a lot. Yes
marioe911116 در تاریخ دوشنبه ۲۷ دسامبر ۲۰۲۱ ساعت ۳:۱۶:۱۴ (UTC+3:30) نوشت:
Reply all
Reply to author
Forward
0 new messages