From: Asmi Mahmood (asmi_mahmood_at_yahoo.com)
Date: Wed Sep 23 2020 - 09:36:52 CDT
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 advaceSent from Yahoo Mail on Android
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