Error in gmx_MMPBSA

[Prarambh Dwivedi]

Hii,

I am getting an issue with running gmx_MMPBSA. Earlier on the same file there was no error with the same command line, but now it displays error. I reinstalled gmx_MMPBSA but error still remains.

Please help

Thank you

input  command:

gmx_MMPBSA -O -i mmpbsa.in -cs md_0_200.tpr -ci index.ndx -cg 1 13 -ct md_0_200_center.xtc -cp topol.top -o mmpbsa -eo energy.csv -deo residue.csv

Execution:

[INFO   ] Starting gmx_MMPBSA v1.5.7

[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs md_0_200.tpr -ci index.ndx -cg 1 13 -ct md_0_200_center.xtc -cp topol.top -o mmpbsa -eo energy.csv -deo residue.csv

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

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/ngsm/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/ngsm/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/ngsm/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/ngsm/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /usr/local/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 1_13 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 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 13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO   ] Checking the structures consistency...
[INFO   ]
[INFO   ] Using topology conversion. Setting radiopt = 0...
[INFO   ] Building Normal Complex Amber topology...
  File "/home/ngsm/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/ngsm/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/ngsm/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 548, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/ngsm/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 118, in buildTopology
    tops = self.gmxtop2prmtop()
  File "/home/ngsm/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 478, in gmxtop2prmtop
    com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
  File "/home/ngsm/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 765, in cleantop
    rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
  File "/home/ngsm/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
    self.read(fname, defines, parametrize)
  File "/home/ngsm/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 377, in read
    atoms[0].exclude(a)
  File "/home/ngsm/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/topologyobjects.py", line 931, in exclude
    raise MoleculeError("Cannot exclude an atom from itself! "
MoleculeError: Cannot exclude an atom from itself! Atoms are: <Atom CL1 [0]; In UNK 0> <Atom CL1 [0]; In UNK 0>
Exiting. All files have been retained.

[marioe911116]

Seems there is something wrong with the topology... could you send us the files you re using to take a closer look?