PDBError

[shilpa sharma]

Hi all,

I am trying to calculate the protein-protein interaction energy for the last 20 ns of simulation with gmx_MMPBSA but I am getiing the following error:

(gmx_mmpbsa23) [sharma69@submit model1]$ gmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ci index.ndx -cg 17 18 -ct final_nojump.xtc -cp topol.top -cr first_frame.pdb
[INFO   ] Starting gmx_MMPBSA v1.6.2
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ci index.ndx -cg 17 18 -ct final_nojump.xtc -cp topol.top -cr first_frame.pdb

tets
[INFO   ] Checking mmpbsa.in input file...
[INFO   ] Checking mmpbsa.in input file...Done.

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /tank/data/LS/saha6/conda/envs/gmx_mmpbsa23/bin/cpptraj
[INFO   ] tleap found! Using /tank/data/LS/saha6/conda/envs/gmx_mmpbsa23/bin/tleap
[INFO   ] parmchk2 found! Using /tank/data/LS/saha6/conda/envs/gmx_mmpbsa23/bin/parmchk2
[INFO   ] sander found! Using /tank/data/LS/saha6/conda/envs/gmx_mmpbsa23/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /sharedapps/spack/opt/spack/linux-rhel8-zen2/gcc-9.5.0/gromacs-2023-ihdgyftcl7cw7dioevipdadksccumpgs/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 chA_chB (17_18) 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 Receptor: Saving group chA (17) 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 chB (18) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
  File "/tank/data/LS/saha6/conda/envs/gmx_mmpbsa23/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/tank/data/LS/saha6/conda/envs/gmx_mmpbsa23/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/tank/data/LS/saha6/conda/envs/gmx_mmpbsa23/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 682, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/tank/data/LS/saha6/conda/envs/gmx_mmpbsa23/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
    self.gmx2pdb()
  File "/tank/data/LS/saha6/conda/envs/gmx_mmpbsa23/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 508, in gmx2pdb
    self.ref_str = check_str(self.FILES.reference_structure, ref=True)
  File "/tank/data/LS/saha6/conda/envs/gmx_mmpbsa23/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 499, in check_str
    refstr = parmed.read_PDB(structure)
  File "/tank/data/LS/saha6/conda/envs/gmx_mmpbsa23/lib/python3.9/site-packages/parmed/formats/pdb.py", line 376, in parse
    inst._parse_open_file(fileobj)
  File "/tank/data/LS/saha6/conda/envs/gmx_mmpbsa23/lib/python3.9/site-packages/parmed/formats/pdb.py", line 430, in _parse_open_file
    method_dispatch[rec](line)
  File "/tank/data/LS/saha6/conda/envs/gmx_mmpbsa23/lib/python3.9/site-packages/parmed/formats/pdb.py", line 703, in _end_model
    raise PDBError('Coordinate mismatch in model %d' % self._current_model_number)
PDBError: Coordinate mismatch in model 1

In my knowledge I have provided the correct files for the calculations and .log file is also not providing any error info. Please help me out in solving this error.

Kind Regards,

Shilpa Sharma

[gmx_MMPBSA]

Seems there is an issue with the reference structure I will say... Please, try without the -cr reference structure flag and see it that works... If you still want to use the reference structure, please feel free to send us the files you are using to see if we can detect the issue

[shilpa sharma]

Yes, the problem is solved now by omitting -cr flag. Thanks for helping me out.

Kind regards,

Shilpa