# gmx\_MMPBSA for big molecule **URL:** \ **Category:** User discussions\ **Created:** [July 10, 2026, 5:23am UTC](https://gromacs.bioexcel.eu/t/gmx-mmpbsa-for-big-molecule/13589 "2026-07-10T05:23:05Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![Diahdd96](https://avatars.discourse-cdn.com/v4/letter/d/ba9def/32.png) [@Diahdd96](https://gromacs.bioexcel.eu/u/Diahdd96)\ **Post date:** [July 10, 2026, 5:23am UTC](https://gromacs.bioexcel.eu/t/gmx-mmpbsa-for-big-molecule/13589/1 "2026-07-10T05:23:05Z")
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 [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 ---
**Author:** ![mevaldes](https://avatars.discourse-cdn.com/v4/letter/m/8797f3/32.png) [@mevaldes](https://gromacs.bioexcel.eu/u/mevaldes)\ **Post date:** [July 10, 2026, 6:30pm UTC](https://gromacs.bioexcel.eu/t/gmx-mmpbsa-for-big-molecule/13589/2 "2026-07-10T18:30:38Z")
Probably no need to rerun the simulation. Can you open an issue here, and include the files you are using in a shared folder? No need to include the whole trajectory; 5 frames are more than enough. > **[Issues · Valdes-Tresanco-MS/gmx\_MMPBSA](https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues)** > > gmx\_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files. - Issues · Valdes-Tresanco-MS/gmx\_MMPBSA