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

From: Jason Swails (
Date: Mon Apr 14 2014 - 07:26:59 CDT

On Mon, 2014-04-14 at 09:56 +0400, James Starlight wrote:
> 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)?

Yes. The "chamber" program has been expanded to support multiple CHARMM
stream files (assuming you set RTF and parameter sections in a stream
file for your system via cgenff). The "" program now
supports topology files created with chamber (neither of these are true
for AmberTools 13). Furthermore, the upcoming chamber release should
support PSF files created with VMD.

> As I noticed amber need slightly shorter cutoffs for non-bonded terms
> in comparison to charm indication difference in this terms between
> both force fields.

Those are just different conventions. The cutoff only applies to the
van der Waals term (as PME includes the full long-range electrostatics
over all periodic images). As long as the particle density reaches
approximately bulk outside of the cutoff, then the long-range dispersion
correction will correct the energy and virial to eliminate the effect of
a cutoff and the net force from all particles beyond the cutoff will be
zero assuming an isotropic distribution of particles at the bulk
densities. For implicit solvent calculations, you should be using an
infinite cutoff anyway (as is convention in Amber).


Jason M. Swails
Rutgers University
Postdoctoral Researcher

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