Error in gmx_MMPBSA Post processing analysis

[Sarthak Trivedi SVNIT]

Hello researchers,

I am facing error in gmx_MMPBSA calculations. I directly copied a script from official page of input (mmpbsa.in) file and put it into the working directory. All the necessary files, carried out from the molecular dynamics simulations of protein ligand complex, are already there in the working directory along with the input file (mmpbsa.in). The list of files are as below.

MD Trajectory file: md_0_10_center.xtc

tpr file: md_0_10.tpr

index file: index.ndx

ligand file: unl.mol2

THE ERROR DESCRIPTION IS AS SHOWN BELOW.

(base) drr-18@drr18-203:~/MD_4B05/MD_Complex/Complex_04$ gmx_MMPBSA -O -i mmpbsa.in -cs md_0_10.tpr -ci index.ndx -cg 1 13 -ct md_0_10_center.xtc -lm unl.mol2 -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
[INFO   ] Starting gmx_MMPBSA v1.5.7
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs md_0_10.tpr -ci index.ndx -cg 1 13 -ct md_0_10_center.xtc -lm unl.mol2 -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

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

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/drr-18/miniconda3/bin/cpptraj
[INFO   ] tleap found! Using /home/drr-18/miniconda3/bin/tleap
[INFO   ] parmchk2 found! Using /home/drr-18/miniconda3/bin/parmchk2
[INFO   ] sander found! Using /home/drr-18/miniconda3/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /usr/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   ] Generating ligand parameters from unl.mol2 file...
[ERROR  ] MMPBSA_Error /home/drr-18/miniconda3/bin/parmchk2 failed when querying unl.mol2.
           Check the gmx_MMPBSA.log file to report the problem.
  File "/home/drr-18/miniconda3/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/drr-18/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/drr-18/miniconda3/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/drr-18/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 116, in buildTopology
    self.gmx2pdb()
  File "/home/drr-18/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 293, in gmx2pdb
    GMXMMPBSA_ERROR('%s failed when querying %s' % (parmchk2, self.FILES.ligand_mol2))
  File "/home/drr-18/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in __init__
    raise exc(msg + '\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error: /home/drr-18/miniconda3/bin/parmchk2 failed when querying unl.mol2
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.

THANKS IN ADVANCE.

[marioe911116]

Please, use the -cp topol.top flag... that way the mol2 is not needed