Thank you for the answers.
We did run the MMGBSA calculation using the CHARMM gbsw method which gave
us reasonable results.
Since we are not aware of any CHARMM modules that can do per-residue energy
decomposition and incorporate entropy, we want to use MMPBSA.py to do this.
Just to note, we are running MMPBSA.py using minimized pdb files from
CHARMM MMGBSA calculations. Could the minimization also be done using
MMPBSA.py package?
Thanks,
Ara
On Fri, Aug 21, 2015 at 11:10 AM, David A Case <david.case.rutgers.edu>
wrote:
> On Fri, Aug 21, 2015, Jason Swails wrote:
> > >
> > > I want to do mmpb(gb)sa calculations for a protein/ligand "dry" complex
> > > using MMPBSA.py package with CHARMM c36 topology/parameter and
> coordinate
> > > files.
>
> Just a note: this combination has not been tested much (or at all?) as
> far as I know. The modfied Bondi radii that seem to work OK for Amber
> charge models are probably OK (TM) for PB calculations using the CHARMM
> charge models. It is much less likely that the Amber GB parameters would
> work all that well for CHARMM potentials: unlike PB, which involves
> only the specification of rather generic atomic radii), GB has lots of
> "shielding" and other adjustable parameters whose values may not be so
> easily transferred to CHARMM force fields.
>
> Since you already have a CHARMM files, (and, presumably, ran the simulation
> in CHARMM or NAMD or something), why not use CHARMM's GB models to do the
> MM-GBSA analysis?
>
> ....dac
>
>
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>
--
Ara
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Received on Fri Aug 21 2015 - 09:00:05 PDT
