Hi, I want to perform MMPBSA for complex file
Command: gmx_MMPBSA -O -i mmpbsa.in -cs md_100.tpr -ct md_center.xtc -ci index.ndx -cg 1 13 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
Error: [INFO ] Starting gmx_MMPBSA v1.6.2 [INFO ] Command-line gmx_MMPBSA -O -i mmpbsa.in -cs md_100.tpr -ct md_center.xtc -ci index.ndx -cg 1 13 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
tets [INFO ] Checking mmpbsa.in input file... [INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs... [INFO ] cpptraj found! Using /home/amjesh/miniconda3/envs/gmxMMPBSA/bin/cpptraj [INFO ] tleap found! Using /home/amjesh/miniconda3/envs/gmxMMPBSA/bin/tleap [INFO ] parmchk2 found! Using /home/amjesh/miniconda3/envs/gmxMMPBSA/bin/parmchk2 [INFO ] sander found! Using /home/amjesh/miniconda3/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_UNK (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 UNK (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb [INFO ] Checking the structures consistency... [ERROR ] MMPBSA_Error
The LP pseudo-atom is not supported. Please remove them following these instructions: https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/Protein_ligand_LPH_atoms_CHARMMff
Check the gmx_MMPBSA.log file to report the problem. File "/home/amjesh/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module> sys.exit(gmxmmpbsa()) File "/home/amjesh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa app.make_prmtops() File "/home/amjesh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 682, in make_prmtops self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology() File "/home/amjesh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology self.gmx2pdb() File "/home/amjesh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 514, in gmx2pdb self.check_structures(self.complex_str, self.receptor_str, self.ligand_str) File "/home/amjesh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1368, in check_structures check_str(com_str) File "/home/amjesh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 513, in check_str GMXMMPBSA_ERROR('The LP pseudo-atom is not supported. Please remove them following these instructions: ' File "/home/amjesh/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:
The LP pseudo-atom is not supported. Please remove them following these instructions: https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/Protein_ligand_LPH_atoms_CHARMMff
Check the gmx_MMPBSA.log file to report the problem.
We followed the instruction that mentioned in above link. Still the error didn't resolve. How to solve this error?
