Re: [AMBER] copy charges using Python API

From: Thomas Evangelidis <>
Date: Mon, 8 Aug 2016 12:00:44 +0200

On 7 August 2016 at 18:13, David A Case <> wrote:

> On Sun, Aug 07, 2016, Thomas Evangelidis wrote:
> >
> > Another question: is anyone aware of any effort made to parallelize
> > antechamber computations? I want to screen a database using bcc charges.
> You should consider doing the parallelization in a script of your own:
> antechamber works with a single molecule (from your database) at a time,
> so you can write a little script that sends each job to a different
> processor.
> Also: see note #7 on p. 277 of the Amber16 Reference Manual: if you have
> good input geometries in your database, you can greatly speed up
> antechamber
> by turning off geometry optimization. Applying the modifications in both
> note 6 and note 7 is often a good option.
​Thanks for the tip!​

​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?


Thomas Evangelidis
Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic

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Received on Mon Aug 08 2016 - 03:30:03 PDT
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