Valdes-Tresanco-MS / gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/
GNU General Public License v3.0
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[Bug-gmx_MMPBSA]: Different version of Gromacs was incompatible with gmxMMPBSA #492

Closed yesyb closed 7 months ago

yesyb commented 7 months ago

Bug summary

Hi, I am trying to calculate the mmpbsa between a protein and peptide. I used gromacs2023.02 and the pbc was removed from the trajectory. But since the version of gmx_MMPBSA is compatible with Gromacs2020, md_2020.tpr was regenerated through the following command: gmx_mpi grompp -f md.mdp -c md.gro -p complex.top -e md.edr -o md_2020.tpr I used the following command to calculate the mmpbsa:
mpirun -np 10 gmx_MMPBSA MPI -O -i mmpbsa1.in -cs md_2020.tpr -ci md.ndx -cg 17 18 -ct md.xtc -cp complex.top However, it gives me the following error MMPBSA_Error: /share/apps/gpu_gromacs/bin/gmx trjconv failed when querying md_C2.xtc
Any help would be appreciated. Thanks!

Terminal output

[INFO   ] Starting gmx_MMPBSA v1.5.0.2
[INFO   ] Command-line
  mpirun -np 10 gmx_MMPBSA MPI -O -i mmpbsa1.in -cs md_2020.tpr -ci md.ndx -cg 17 18 -ct md_C2.xtc -cp complex.top

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/jq/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/jq/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/jq/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/jq/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /share/apps/gpu_gromacs/bin/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 17_18 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[ERROR  ] MMPBSA_Error /share/apps/gpu_gromacs/bin/gmx trjconv failed when querying md_C2.xtc.
           Check the gmx_MMPBSA.log file to report the problem.
  File "/home/jq/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/jq/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
    app.make_prmtops()
  File "/home/jq/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 535, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/jq/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 116, in buildTopology
    self.gmx2pdb()
  File "/home/jq/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 232, in gmx2pdb
    GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(comprog), self.FILES.complex_trajs[0]))
  File "/home/jq/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in __init__
    raise exc(msg + '\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error: /share/apps/gpu_gromacs/bin/gmx trjconv failed when querying md_C2.xtc
Check the gmx_MMPBSA.log file to report the problem.
Error occurred on rank 0.
Exiting. All files have been retained.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

gmx_MMPBSA.log

gmx_MMPBSA.log

Operating system

UBUNTU

gmx_MMPBSA Version

1.5.0.2

Python version

3.9

Installation

None

yesyb commented 7 months ago

Here are the Tpr file and trajectory file used to calculate PBSA, as the trajectory file was too large, I chose the last 5ns to upload. Looking forward to your response! Thank you! calculate.zip