[Bug-gmx_MMPBSA]: bad atom type error when calculating complex contribution

2222A commented 1 year ago

Bug summary

Hi,I calculate a system with LPH followed the tutorial,but it occur bad atom type error (bad atom type :IG) when program calculate complex contribution.

Terminal output

[INFO   ] Starting gmx_MMPBSA v1.6.1
[INFO   ] Command-line
  mpirun -np 8 gmx_MMPBSA MPI -O -i mmpbsa2.in -cs mass.pdb -ci index.ndx -cg 1 13 -ct trj_orgin.xtc -cp topol.top -o final_results.dat -eo final_result_mmpbas.csv

[INFO   ] Checking mmpbsa2.in input file...
[INFO   ] Checking mmpbsa2.in input file...Done.

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /opt/miniconda3/envs/gmxmmpbsa/bin/cpptraj
[INFO   ] tleap found! Using /opt/miniconda3/envs/gmxmmpbsa/bin/tleap
[INFO   ] parmchk2 found! Using /opt/miniconda3/envs/gmxmmpbsa/bin/parmchk2
[INFO   ] sander found! Using /opt/miniconda3/envs/gmxmmpbsa/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /opt/miniconda3/envs/gmxmmpbsa/bin.AVX2_256/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_LIG (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 LIG (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_pb2 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_pb2 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_pb2 to Ligand...
[INFO   ] Writing Normal Ligand AMBER topology...
[INFO   ] User-selected residues for decomposition analysis...
[INFO   ] Selected 19 residues:
R:A:ARG:64  R:A:THR:81  R:A:ASP:84  R:A:ILE:85  R:A:SER:88  R:A:SER:89  R:A:PHE:93  R:A:VAL:131 R:A:PRO:132 R:A:PHE:135
R:A:PHE:167 R:A:THR:175 R:A:THR:178 R:A:SER:179 R:A:TRP:245 R:A:PHE:248 R:A:ILE:271 R:A:TYR:275 L:B:LIG:300

[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   ] 10 frames were processed by cpptraj for use in calculation.
tets

[INFO   ] Starting calculations in 8 CPUs...
[INFO   ] Running calculations on normal system...
[INFO   ] Beginning GB calculations with /opt/miniconda3/envs/gmxmmpbsa/bin/sander
[INFO   ]   calculating complex contribution...
              0%|          | 0/10 [elapsed: 00:00 remaining: ?] bad atom type: IG
  File "/opt/miniconda3/envs/gmxmmpbsa/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/opt/miniconda3/envs/gmxmmpbsa/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
    app.run_mmpbsa()
  File "/opt/miniconda3/envs/gmxmmpbsa/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 205, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/opt/miniconda3/envs/gmxmmpbsa/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 142, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/opt/miniconda3/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: /opt/miniconda3/envs/gmxmmpbsa/bin/sander failed with prmtop COM.prmtop!
Error occurred on rank 7.
Exiting. All files have been retained.
Abort(1) on node 7 (rank 7 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 7

gmx_MMPBSA.log

Operating system

CentOS 7

gmx_MMPBSA Version

1.6.1

Python version

3.9.15

Installation

None

Valdes-Tresanco-MS commented 1 year ago

GB only supports a few pre-defined atoms that allow energetic decomposition. In this case, IG is not supported. You can see more related information here. This happens because the method you use to estimate the nonpolar component of solvation (SASA) requires the radius of vdw (independent of solvation radius), which is predefined in the sander source code and not in the topology. You can try just with PB, in this case, it should work.

2222A commented 1 year ago

OK,thx,i will try and feedback.

2222A commented 1 year ago

Yes,PB method worked!

Valdes-Tresanco-MS / gmx_MMPBSA