GROMACS version: 2018
I tried several times on fixing error of gmx_MMPBSA for protein 3VSL (s.aureus) with claude.ai but it seemed endless. the error look like this :
[INFO ] parmchk2 found! Using /home/diah/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/diah/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/diah/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/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 Protein_UNN (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Generating ligand parameters from Baicalein_7-O-Glucuronide_bcc_gaff2.mol2 file…
[INFO ] No receptor structure file was defined. Using ST approach…
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (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 UNN (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Checking the structures consistency…
[INFO ] Generating AMBER Compatible PDB Files…
[INFO ] Changing the Complex residues name format from GROMACS to AMBER…
[INFO ] Changing the Receptor residues name format from GROMACS to AMBER…
[INFO ] Changing the Ligand residues name format from GROMACS to AMBER…
[INFO ] Splitting receptor and ligand in PDB files..
[INFO ] Building tleap input files…
[INFO ] Cleaning normal complex trajectories…
[INFO ] Building AMBER topologies from GROMACS files… Done.
[INFO ] Loading and checking parameter files for compatibility…
[INFO ] Preparing trajectories for simulation…
Error: # atoms in XTC file (9979) does not match # atoms in parm COM.prmtop (9982)
Error: Could not set up ‘COM_traj_0.xtc’ for reading.
Error: Could not set up input trajectory ‘COM_traj_0.xtc’.
Error: Error(s) occurred during execution.
File “/home/diah/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA”, line 8, in
sys.exit(gmxmmpbsa())
^^^^^^^^^^^
File “/home/diah/miniconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/app.py”, line 100, in gmxmmpbsa
app.file_setup()
File “/home/diah/miniconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/main.py”, line 138, in file_setup
lig_frames, self.numframes_nmode) = make_trajectories(INPUT, FILES, self.mpi_size,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/diah/miniconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/make_trajs.py”, line 68, in make_trajectories
traj = Trajectory(FILES.complex_prmtop, FILES.complex_trajs, cpptraj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/diah/miniconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/make_trajs.py”, line 508, in _init_
self.Query()
File “/home/diah/miniconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/make_trajs.py”, line 643, in Query
raise TrajError('%s failed when querying %s' % (self.exe, traj))
TrajError: /home/diah/miniconda3/envs/gmxMMPBSA/bin/cpptraj failed when querying COM_traj_0.xtc
Error occurred on rank 0.
Exiting. All files have been retained.
Abort(1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
(gmxMMPBSA) diah@Diah-PC:/run/media/diah/260A-AEE4/MD KENCANA UNGU/MD_3VSL_Bai/MMPB_GBSA$
it seemed that there is missmatch of atom number in prmtop with XTC file, if there is error like this, should we redo the simulation, since the XTC file is resulted from mdrun, or we can just adjust the xtc or topol file (like claude.ai suggested)? please let me know