Re: [AMBER] about reproduction of HIS RESP charge

From: FyD <>
Date: Thu, 18 Oct 2012 21:39:39 +0200

Dear Jocelyne,

> I would like to create a topology for my system which has a mutant
> residue. Before working on mutant, I just want to reproduce RESP
> charge of residue which is HIS . 
> How can I reproduce RESP of HIS for ff99SB?

This topic has been discussed several times in the Amber mailing list.

You can learn how to generate RESP charges for the central fragment of
the histidine residue; but you will not be able to reproduce the
charge values available in the Amber Force Field Topology DataBase

The main problem comes from the molecular orientation of the optimized
geometry used to compute the molecular electrostatic potential (MEP)
which is not rigorously controlled. To solve this problem the R.E.D.
program has been developed and the charge values reproducibility
obtained is around of 1.10-4 e. This means if you decide to use R.E.D.
and you rigorously define and report the computational conditions used
in MEP computation (i.e. mainly the molecular orientation(s) for a
given conformation) other users will be able to reproduce your
published data but you will NEVER be able to reproduce the charge
values available in the Amber FFTopDB).

See &
the "Charge reproducibility" section at

> If I can manage it I can also produce RESP of mutant residue. Is it
> possible to do that? or is there some bias parameter in there?

You could use the tutorials at; see for instance:
  and finally

regards, Francois

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Received on Thu Oct 18 2012 - 13:00:04 PDT
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