Re: MMPBSA Energy Calculations using VMD (Post-Processing)

From: Jason Swails (
Date: Sat Apr 12 2014 - 06:53:32 CDT

On Sat, Apr 12, 2014 at 2:53 AM, James Starlight <>wrote:

> Dear all,
> I also looking for the possibility to calculate free energy of ligand
> binding using script and NAMD trajectory.
> As I know in NAMD I can make parametrization of my system using amber (not
> charmm) force field. So I need (i) proper way to parametrize ligand in
> amber (ii) convert dcd to amber-like trajectory

For (i) you can use antechamber from AmberTools. Your step (ii) is
unnecessary. understands DCD files natively.

Also, if you've used the CHARMM force field and created the PSF file with
VMD, the upcoming release of AmberTools 14 (within a week) will have a
version of "chamber" that can convert VMD-generated PSF files into topology
files can understand.

Hope this helps,

Jason M. Swails
Rutgers University
Postdoctoral Researcher

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