Re: [AMBER] What is the default pH when loading a protein in Amber environment

From: Carlos Simmerling <>
Date: Wed, 11 Mar 2020 07:48:30 -0400

Once you determine the protons tion states of each residue (which depends
on pH) you would change the residue names to use the alternate version. For
example, HIP, ASH, GLH. You might want to look at the H++ web site and
instructions for more info.

On Wed, Mar 11, 2020, 7:21 AM Siavoush Dastmalchi <>

> Dear list,
> I want to do an MD simulation with a protein at pH 8, but without using
> "constant pH simulation" method described in tutorials like "Advanced
> Tutorial 18". I was wondering when a protein is loaded in amber
> environment, what are the protonation states of the residue side chains. I
> suppose it should be the protonation state at neutral pH. Now the question
> is if I want to start with a structure at a different pH, such as 5 where
> the protonation state of residues such as His is different than that in pH
> 7, how I can tell this to Amber to consider the protonation states at the
> required pH. In other words, is there any command in amber to prepare the
> structure of a protein at a given pH.
> Cheers,
> Siavoush
> *************************************************
> Siavoush Dastmalchi
> Professor of Medicinal Chemistry
> Director of Biotechnology Research Center &
> Head of Medicinal Chemistry Department
> Tabriz University of Medical Sciences
> Tabriz-Iran
> Tel: +98(41)33364038
> Fax: +98(41)33379420
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Received on Wed Mar 11 2020 - 05:00:01 PDT
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