Re: [AMBER] how to Neutralize system automatically?

From: Eric Lang <>
Date: Fri, 27 Jan 2017 11:34:35 +0000

If you set 0 for the number of ions to add, the number of ions needed to
neutralise the system will be automatically added.
Be careful however with the rounding of the net charge of the system. Have
a look in the manual in the leap section.

On 27 January 2017 at 10:00, Albert <> wrote:

> Hello,
> I've got hundred of compounds to be simulated in Amber. I would like to
> automatize the system building procedure. However, each ligand contains
> different total charge. I am just wondering is there any command line or
> options in Amber to neutralize the charge automatically? Currently, I
> have to first run "charge" command, then add ions according to the results.
> Thx a lot
> Albert
> _______________________________________________
> AMBER mailing list

Eric Lang
BrisSynBio Postdoctoral Research Associate Modelling
Centre for Computational Chemistry
School of Chemistry - University of Bristol
Bristol BS8 1TS - United Kingdom
AMBER mailing list
Received on Fri Jan 27 2017 - 04:00:03 PST
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