error in running interaction entropy

[parul goyal]

when i am entering this input command to find interaction entropy :

gmx_MMPBSA -O -i mmpbsa_new_entropy.in -cs npt.tpr -ci index.ndx -cg 19 20 -ct md.xtc -o FINAL_RESULTS_MMPBSA_1.dat -eo FINAL_RESULTS_MMPBSA_1.csv

[INFO   ] Starting gmx_MMPBSA v1.5.6+25.g309d2fe
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa_new_entropy.in -cs npt.tpr -ci index.ndx -cg 19 20 -ct md.xtc -o FINAL_RESULTS_MMPBSA_1.dat -eo FINAL_RESULTS_MMPBSA_1.csv

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

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/parul/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/parul/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/parul/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/parul/anaconda3/envs/gmxMMPBSA/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 19_20 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 19 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 20 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[ERROR  ] MMPBSA_Error gmx_MMPBSA does not support water/ions molecules in any structure, but we found 73 molecules in the complex..
           Check the gmx_MMPBSA.log file to report the problem.
  File "/home/parul/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/parul/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/parul/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 545, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/parul/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 116, in buildTopology
    self.gmx2pdb()
  File "/home/parul/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 415, in gmx2pdb
    self.check4water()
  File "/home/parul/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 437, in check4water
    GMXMMPBSA_ERROR(f'gmx_MMPBSA does not support water/ions molecules in any structure, but we found'
  File "/home/parul/anaconda3/envs/gmxMMPBSA/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: gmx_MMPBSA does not support water/ions molecules in any structure, but we found 73 molecules in the complex.
Check the gmx_MMPBSA.log file to report the problem.

Exiting. All files have been retained in log file.

npt.tpr is md.tpr actually but i checked mine index file it as seems fine then why error,can any body pls help me out.

[parul goyal]

should i change mine parameters to -cg to 1 13 instead of 19 20 as mine ligand and receptor as this position in index file

[Mario Sergio Valdes]

Yes, in the example the groups are 19 and 20, however, you must use the appropriate ones in your system. You can check them in your index file (gmx make_ndx -n index.ndx). Commonly for protein-ligand systems, these groups are 1 and 13