Re: [AMBER] Reg: MMGBSA for NAMD trajectory

From: David A Case <>
Date: Wed, 11 Mar 2020 14:20:43 -0400

On Wed, Mar 11, 2020, Lara rajam wrote:

>Is it possible to perform MMGBSA for the simulation carried out using
>NAMD-CHARMM force field?

Yes and no.

Techically, you could use the "chamber" action in ParmEd to convert
a CHARMM setup to Amber, then run all of our programs in the usual way.

The glitch is that Amber's GB models have been optimized for Amber's
force fields, and we don't offer implicit solvent models that are tuned
for CHARMM force fields. My guess is that your best path, if you want to
stick with CHARMM force fields, is to carry out the analysis in CHARMM
as well, using their implicit solvent models.


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Received on Wed Mar 11 2020 - 11:30:02 PDT
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