[Question]: Bad atom type #616
Description
My Question is...
(gmxMMPBSA) [ssingh@master corr_hb]$ gmx_MMPBSA -O -i mmpbsa.in -cs md_0_10.tpr -ct md_noPBC.xtc -ci ind_new.ndx -cg 21 14 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -do FINAL_DECOMP_MMPBSA.dat -deo FINAL_DECOMP_MMPBSA.csv [INFO ] Starting gmx_MMPBSA 1.6.4 [INFO ] Command-line gmx_MMPBSA -O -i mmpbsa.in -cs md_0_10.tpr -ct md_noPBC.xtc -ci ind_new.ndx -cg 21 14 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -do FINAL_DECOMP_MMPBSA.dat -deo FINAL_DECOMP_MMPBSA.csv [INFO ] Checking mmpbsa.in input file... [INFO ] Checking mmpbsa.in input file...Done. [INFO ] Checking external programs... [INFO ] cpptraj found! Using /scratch/home/ssingh/miniconda/envs/gmxMMPBSA/bin/cpptraj [INFO ] tleap found! Using /scratch/home/ssingh/miniconda/envs/gmxMMPBSA/bin/tleap [INFO ] parmchk2 found! Using /scratch/home/ssingh/miniconda/envs/gmxMMPBSA/bin/parmchk2 [INFO ] sander found! Using /scratch/home/ssingh/miniconda/envs/gmxMMPBSA/bin/sander [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx_mpi found! Using /scratch/home/ssingh/apps/gromacs_cpu/bin/gmx_mpi [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 rec_LIG (21_14) 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 rec (21) 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 (14) 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 Amber/OPLS force field topology format... [WARNING] 74 invalid DIHEDRAL_PERIODICITY = 0 found in Complex topology... Setting DIHEDRAL_PERIODICITY = 1 [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 3 residues: R:A:HIS:122 R:A:ASP:126 L:E:LIG:149 [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 ] 10001 frames were processed by cpptraj for use in calculation. [INFO ] Starting calculations in 1 CPUs... [INFO ] Running calculations on normal system... [INFO ] Beginning GB calculations with /scratch/home/ssingh/miniconda/envs/gmxMMPBSA/bin/sander [INFO ] calculating complex contribution... 0%| | 0/10001 [elapsed: 00:00 remaining: ?] bad atom type: FE File "/scratch/home/ssingh/miniconda/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 7, in sys.exit(gmxmmpbsa()) ^^^^^^^^^^^ File "/scratch/home/ssingh/miniconda/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa app.run_mmpbsa() File "/scratch/home/ssingh/miniconda/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/main.py", line 205, in run_mmpbsa self.calc_list.run(rank, self.stdout) File "/scratch/home/ssingh/miniconda/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/calculation.py", line 142, in run calc.run(rank, stdout=stdout, stderr=stderr) File "/scratch/home/ssingh/miniconda/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/calculation.py", line 284, in run raise CalcError(f'{self.program} failed with prmtop {self.prmtop}!') CalcError: /scratch/home/ssingh/miniconda/envs/gmxMMPBSA/bin/sander failed with prmtop COM.prmtop! Exiting. All files have been retained. (gmxMMPBSA) [ssingh@master corr_hb]$