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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Received on Fri Aug 21 2015 - 08:30:05 PDT
