Error of parameter file compatibility issues in Interaction Entropy Corrections

[Sarthak Trivedi SVNIT]

Hello sir, 

I have received an error regarding the Interaction entropy calculations. I am attaching input file over here and mentioning the error. 

(gmxMMPBSA) drr-18@drr18-System-Product-Name:~/Complex_02_50ns_MMPBSA$ mpirun -np 8 gmx_MMPBSA MPI -O -i nmode.in -cs md_0_10.tpr -ci index.ndx -cg 1 13 -ct md_0_10_center.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
[INFO   ] Starting gmx_MMPBSA v1.6.1
[INFO   ] Command-line
  mpirun -np 8 gmx_MMPBSA MPI -O -i nmode.in -cs md_0_10.tpr -ci index.ndx -cg 1 13 -ct md_0_10_center.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

[INFO   ] Checking nmode.in input file...
[WARNING] Default DRMS value is 0.001! However 2.0 is being used. Check documentation for more details...
[INFO   ] Checking nmode.in input file...Done.

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/drr-18/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/drr-18/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/drr-18/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/drr-18/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] mmpbsa_py_nabnmode found! Using /home/drr-18/miniconda3/envs/gmxMMPBSA/bin/mmpbsa_py_nabnmode
[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 Protein_UNL (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 Protein (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 UNL (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...
[INFO   ] Detected CHARMM force field topology format...
[INFO   ] Assigning PBRadii mbondi to Complex...
[INFO   ] Writing Normal Complex AMBER topology...
[INFO   ] No Receptor topology file was defined. Using ST approach...
[INFO   ] Building AMBER Receptor topology from Complex...
[INFO   ] Assigning PBRadii mbondi to Receptor...
[INFO   ] Writing Normal Receptor AMBER topology...
[INFO   ] No Ligand topology file was defined. Using ST approach...
[INFO   ] Building AMBER Ligand topology from Complex...
[INFO   ] Assigning PBRadii mbondi to Ligand...
[INFO   ] Writing Normal Ligand AMBER topology...
[INFO   ] Cleaning normal complex trajectories...
[INFO   ] Building AMBER topologies from GROMACS files... Done.

[INFO   ] Loading and checking parameter files for compatibility...
[ERROR  ] MMPBSA_Error

CHAMBER prmtops cannot be used with NMODE

Check the gmx_MMPBSA.log file to report the problem.
  File "/home/drr-18/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/drr-18/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 99, in gmxmmpbsa
    app.loadcheck_prmtops()
  File "/home/drr-18/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 728, in loadcheck_prmtops
    GMXMMPBSA_ERROR('CHAMBER prmtops cannot be used with NMODE')
  File "/home/drr-18/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
    raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:

CHAMBER prmtops cannot be used with NMODE

Check the gmx_MMPBSA.log file to report the problem.
Error occurred on rank 4.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4

 

[marioe911116]

Unfortunately, and as the output says, NMode is not compatible with Charmm topologies.
We have just looked for other methodologies for NMode calculation that we will try to implement in the future.