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.
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
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
gmx_MMPBSA.log
gmx_MMPBSA.log
Operating system
UBUNTU
gmx_MMPBSA Version
1.5.0.2
Python version
3.9
Installation
None