Hi I'm using AMBER mmpbsa.py for energy calculation of my system. In my protein- ligand system there is also a metal atom Nickle in the binding site. I used charmm-gui for PSF generation and ran simulations using NAMD. For MMPbsa, I used ambertools20. Converted all PSF and crd files into prmtop using commands in parmed of chamber: Chamber -top top.rtf -param file.prm - str file.str -psf file.psf -crd file .PDB
Followed by outparm file.prmtop and inpcrd.
All files generated successfully without any error. But when I ran MMPbsa command it gives error just after initializing GB calculation Calerr: complex.prmtop
Detail of error in gb.out file is FATAL: mismatch NATOM in coordinate and topology file.
For troubleshooting, I ran tutorial files it ran well. In addition I also ran an other NAMD simulated protein. It also ran without any error.
I am confused how to sort it out.I checked number of atoms in complex PSF and PDB files atoms are same. I generted PSF files both by charmm-gui and also by vmd. Even then same error.My gut feel says it's something about the metal ion in the binding site.
Plz guide me. Thanks in advance
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Received on Wed Sep 23 2020 - 23:30:02 PDT
