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

From: James Starlight (
Date: Mon Apr 21 2014 - 14:27:38 CDT

Many thanks for suggestions!

As I've understood from the Amber-14 manual for I'll need one
'dry' dcd trajectory consisted of only protein and ligand and psf topology
which (1) should be converted to amber-like topology by means of 'chamber'
and (2) from which 3 additional topologies will be created by means of
"". Does such workflow correct?

Some questions:
1) What are the reasonable time step for snapshots extractions from the
initial solvated trajectory?
2) Should I convert parametrization of my system done in charm +cgenff to
the amber-like force field including charges distribution?

Thanks again for suggestion,


2014-04-14 22:02 GMT+04:00 Jason Swails <>:

> On Mon, 2014-04-14 at 13:24 -0400, Kenno Vanommeslaeghe wrote:
> > I'm not sure the PBSA radii for AMBER atom types are accurate when used
> > with CHARMM charges.
> >
> > Also, as a reminder, if you use the CHARMM FF for your ligand, you have
> to
> > use the CHARMM FF for your protein as well.
> >
> > Finally, I'd like to point out the "as long as the particle density
> > reaches approximately bulk outside of the cutoff" assumption is not
> always
> > valid. It may not matter for implicit solvent, but I just wanted to have
> > this on the record so that people who work on other things don't get the
> > wrong idea. For instance, membranes in explicit solvent are crazy
> > sensitive to small details in the nonbonded interactions at long range.
> Well sure, but then the assumption of an "isotropic distribution of
> particles beyond the cutoff" breaks down as membrane systems are
> decidedly NOT isotropic.
> For membrane simulations (or surface simulations or simulations with any
> anisotropic particle distribution) I defer to the relevant literature.
> All the best,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher

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