error running gmx_MMPBSA: IndexError: list index out of range

[Anna VERDINO]

Hi, I am performing be calcutaion using gmx_MMPBSA.

First of all   I convert the topology using this commands:

import parmed as pmd

gmx_top = pmd.load_file('topology_bycharmmgui.top')

gmx_top.save('pmaa.top')

Then I lunch this:

gmx_MMPBSA -O -i mmpbsa.in -cs full.tpr -ci complex.ndx -cg 1 15 -ct trj-GALT_G1P_H2U.xtc -cp pmaa1.top -o final.dat -do final2.dat

[WARNING] protein_forcefield and ligand_forcefield variables are deprecate since version 1.4.1 and will be remove in the next version. Please, use forcefield instead.
[WARNING] entropy_seg variable is deprecate since version 1.4.2 and will be remove in v1.5.0. Please, use ie_segment instead.
[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /opt/amber20/bin/cpptraj
[INFO   ] tleap found! Using /opt/amber20/bin/tleap
[INFO   ] parmchk2 found! Using /opt/amber20/bin/parmchk2
[INFO   ] sander found! Using /opt/amber20/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /opt/gromacs-2022.2/bin/gmx
[INFO   ] Checking external programs...Done.

[INFO   ] Building AMBER Topologies from GROMACS files...
[INFO   ] Checking gmxMMPBSA data folder exists in Amber data...
[INFO   ] Get PDB files from GROMACS structures files...
[INFO   ] Making gmx_MMPBSA index for complex...
[INFO   ] Normal Complex: Saving group 1_15 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 Complex: 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 15 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO   ] Building Normal Complex Amber Topology...
  File "/opt/amber20/miniconda/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/opt/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 95, in gmxmmpbsa
    app.make_prmtops()
  File "/opt/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/main.py", line 576, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/opt/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 117, in buildTopology
    tops = self.gmxtop2prmtop()
  File "/opt/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 318, in gmxtop2prmtop
    com_top = self.cleantop(self.FILES.complex_top, self.indexes[0] + self.indexes[1])
  File "/opt/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 602, in cleantop
    if rtemp_top.atoms[i-1].residue.number + 1 not in res_list:
IndexError: list index out of range
Exiting. All files have been retained.

Kindly help me, please.

Thank you.

[marioe911116]

Which version of gmx_MMPBSA are you using?

try updating and see if that solves the issue...

python -m pip install gmx_MMPBSA -U