Re: [AMBER] Query regarding the internal energy of protein.

From: David A Case <>
Date: Mon, 17 Dec 2018 08:34:56 -0500

On Mon, Dec 17, 2018, Leena Aggarwal wrote:
>Any suggestions for calculating the configurational energy of protein from
>total energy of the system.

There is no correct way to do this: the reciprocal portion of the
electrostatic contribution cannot (easily) be divided into pieces.
Also, it's fundamentally unclear what you mean by the "configurational
energy of the protein": where would you put the interaction terms
between protein and solvent?

The MM-PBSA or MM-GBSA methods approach this problem by stripping away
the waters, and substituting back in an implicit solvation term. This
may or may not provide something like what you want.

...good luck...dac

AMBER mailing list
Received on Mon Dec 17 2018 - 06:00:09 PST
Custom Search