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

From: James Starlight (
Date: Mon Apr 14 2014 - 00:56:50 CDT

Many thanks for suggestions!

I'll try to wait AmberTools 14 and test it with the namd's produced
trajectory and all input files.
One question: can I use parametrization of my system done in charm-like
force field instead of amber (including ligand parametrized in cgenff)? As
I noticed amber need slightly shorter cutoffs for non-bonded terms in
comparison to charm indication difference in this terms between both force

Thanks for help,


2014-04-12 15:53 GMT+04:00 Jason Swails <>:

> 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
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher

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