Re: [AMBER] CHARMM 3 extra energy terms in AMBER dynamic engines (SANDER&PMEMD)

From: David A Case <>
Date: Thu, 22 Aug 2019 09:35:19 -0400

On Wed, Aug 21, 2019, Lod King wrote:
>Can someone guide/explain to me how the SANDER or PMEMD engine works for
>CHARMM force field (with additional UB, improper and CMAP energy terms)?
>via CHAMBER or SANDER's and PMEMD's code in AMBER protocol?

What is it that you need to figure out? The "chamber" action in parmed
(which replaces the older "chamber" stand-alone program) converts
psf,etc files coming from CHARMM into Amber-compatible prmtop and
inpcrd files. The sander or pmemd codes recognize from the prmtop file
that this is a CHARMM force field, and compute the appropriate terms.

(Note also that the CHARMM-GUI can output Amber-compatible files
directly: it does this by calling "chamber" in parmed behind the scenes,
so you don't have to do it yourself.)

Of course, there are tons of details involved, but I can't tell from
your question what you are really looking for.


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Received on Thu Aug 22 2019 - 07:00:03 PDT
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