error

negin s

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Dec 24, 2021, 3:09:01 AM12/24/21

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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

[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 ] 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.
Exiting. All files have been retained.

Kindly help me

Thank you

Mario Sergio Valdes

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Dec 24, 2021, 2:43:51 PM12/24/21

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Please, send me the *.mdout.0 files

Mario S.

negin safaee

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Dec 27, 2021, 9:25:12 AM12/27/21

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were the files received?
thank you

Mario Sergio Valdes

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Dec 27, 2021, 12:03:00 PM12/27/21

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Please send me the following missing files: tpr, ndx, and receptor and ligand groups respectively

negin s

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Dec 28, 2021, 10:03:33 AM12/28/21

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Sorry, were the files received?
thank you

Mario Sergio Valdes

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Dec 28, 2021, 10:45:45 AM12/28/21

to gmx_MMPBSA

Hi Negin.

Your system has several problems. The first is that the resulting structure of the tpr is broken. That means that the processing done on it will be inconsistent. This is solved by generating a PDB structure from the trajectory that is consistent and passing it as an argument in the -cs option, instead of the tpr file. Likewise, the trajectory you sent me has PBC. Make sure you don't have PBC, as gmx_MMPBSA does not remove it and you may get inconsistent results. Also, note that the trajectory must be consistent with the defined groups.
From there, everything worked as expected.