bad atom type: IG

[sagar bhayye]

Dear all,

The gmxMMPBSA giving a error related to Iodine atom type. Please find the details in the log file.

Output from terminal.

mpirun -np 6 gmx_MMPBSA -O -i mmpbsa.in -cs str_noLP.pdb -ci index_mod_gromacs.ndx -cg 1 61 -ct com_traj.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
[INFO   ] Starting gmx_MMPBSA v1.6.3
[INFO   ] Command-line
  mpirun -np 6 gmx_MMPBSA -O -i mmpbsa.in -cs str_noLP.pdb -ci index_mod_gromacs.ndx -cg 1 61 -ct com_traj.xtc -cp topol.top -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/sagar/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/sagar/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/sagar/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/sagar/anaconda3/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 Protein_L80_&_!L80_LP1_4288 (1_61) 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 L80_&_!L80_LP1_4288 (61) 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 mbondi2 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 mbondi2 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 mbondi2 to Ligand...
[INFO   ] Writing Normal Ligand AMBER topology...
[INFO   ] Selecting residues by distance (6 Å) between receptor and ligand for decomposition analysis...
[INFO   ] Selected 41 residues:
R:A:ILE:9   R:A:GLY:10  R:A:GLU:11  R:A:GLY:12  R:A:ALA:13  R:A:TYR:14  R:A:GLY:15  R:A:LYS:16  R:A:VAL:17  R:A:PHE:18
R:A:LYS:19  R:A:VAL:30  R:A:ALA:31  R:A:LYS:33  R:A:GLU:44  R:A:LEU:48  R:A:VAL:60  R:A:ARG:61  R:A:LEU:71  R:A:VAL:72
R:A:PHE:73  R:A:GLU:74  R:A:HIS:75  R:A:VAL:76  R:A:ASP:77  R:A:GLN:78  R:A:ASP:79  R:A:THR:81  R:A:ASP:120 R:A:LYS:122
R:A:PRO:123 R:A:GLN:124 R:A:ASN:125 R:A:ILE:126 R:A:LEU:127 R:A:ALA:137 R:A:ASP:138 R:A:PHE:139 R:A:ALA:142 R:A:THR:144
L:B:L80:264

[INFO   ] Cleaning normal complex trajectories...
[INFO   ] Building AMBER topologies from GROMACS files... Done.

[INFO   ] Loading and checking parameter files for compatibility...
[INFO   ] Preparing trajectories for simulation...

[INFO   ] 20001 frames were processed by cpptraj for use in calculation.
[INFO   ] Starting calculations in 6 CPUs...

[INFO   ] Running calculations on normal system...
[INFO   ] Beginning GB calculations with /home/sagar/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO   ]   calculating complex contribution...
              0%|          | 0/20001 [elapsed: 00:00 remaining: ?] bad atom type: IG
 bad atom type: IG
  File "/home/sagar/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/sagar/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
    app.run_mmpbsa()
  File "/home/sagar/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 205, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/sagar/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 142, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/home/sagar/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 284, in run
    raise CalcError(f'{self.program} failed with prmtop {self.prmtop}!')
CalcError: /home/sagar/anaconda3/envs/gmxMMPBSA/bin/sander failed with prmtop COM.prmtop!
Error occurred on rank 1.
Exiting. All files have been retained.
  File "/home/sagar/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/sagar/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
    app.run_mmpbsa()
  File "/home/sagar/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 205, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/sagar/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 142, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/home/sagar/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 284, in run
    raise CalcError(f'{self.program} failed with prmtop {self.prmtop}!')
CalcError: /home/sagar/anaconda3/envs/gmxMMPBSA/bin/sander failed with prmtop COM.prmtop!
Error occurred on rank 4.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4
 bad atom type: IG

Help me out to solve this error.

Thank you.

[mariosergi...@gmail.com]

Please, check this thread https://groups.google.com/g/gmx_mmpbsa/c/YeTDAbXvurQ/m/BToWonT3AQAJ