Re: NAMD trajectory with

From: I. Camps (
Date: Wed Sep 23 2020 - 09:54:08 CDT

It may be a problem during conversion (from my experience: past successful
conversion doesn't imply future successful conversions...).

For MMPBSA calculations from NAMD results, I suggest using CaFE ( CaFE is a VMD plugin that have
two methods to compute DeltaE (



On Wed, Sep 23, 2020 at 11:40 AM Asmi Mahmood <>

> Hi
> I'm using AMBER 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 advace
> Sent from Yahoo Mail on Android
> <>

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