Re: [AMBER] do you know

From: David A Case <>
Date: Sun, 3 Jan 2021 09:16:11 -0500

On Sun, Jan 03, 2021, Gordon Richard Chalmers wrote:

>That almost all, I think, protein structures and models were
>deposited without pre-energy minimization. Not like carbohydrates.
>The RMSD is a little large, .5 to 1 A and then some. The difference
>is in using a physically realistic set of interactions.

You (and others on the list) might be interested in this paper, which shows
one method to refine crystal structures using a force field potential:

%A N.W. Moriarty
%A P.A. Janowski
%A J.M. Swails
%A H. Nguyen
%A J.S. Richardson
%A D.A. Case
%A P.D. Adams
%T Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix
%J Acta Cryst. D
%V 76
%P 51-62
%D 2020
%R doi:10.1107/S2059798319015134

[For those who care: this code behind this illustrates how to use the python
API for sander, and how someone with no knowledge of Amber can run crystal
simulations on a large fraction of the structures in the PDB.]


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Received on Sun Jan 03 2021 - 06:30:03 PST
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