Re: [AMBER] copy charges using Python API

From: David A Case <>
Date: Mon, 8 Aug 2016 08:16:13 -0400

On Mon, Aug 08, 2016, Thomas Evangelidis wrote:
> Regarding the input geometries, I read in the manual that in vacuo
> minimization of anions like phosphates is inappropriate as they may form
> intra-molecular H-bonds. In fact I currently work with such molecules, so
> the question is how to obtain good starting geometries to speed up the
> calculation of AM1 charges? To minimize the structures in implicit solvent
> first using Gasteiger charges and then calculate AM1 charges by setting "
> maxcyc" to a low value?

I don't have any good ideas or experience here. It would seem to depend on
(a) how "good" or "bad" the geometries you already have are; (b) how sensitive
the charges are to changes in geometry; (c) how sensitive your docking or
binding energy calculations are to changes in charges.

You might experiment with different strategies to see how sensitive things


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Received on Mon Aug 08 2016 - 05:30:02 PDT
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