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

From: Siavoush Dastmalchi <dastmalchi.s.tbzmed.ac.ir>
Date: Wed, 11 Mar 2020 14:50:41 +0330

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.


Siavoush Dastmalchi
Professor of Medicinal Chemistry
Director of Biotechnology Research Center &
Head of Medicinal Chemistry Department
Tabriz University of Medical Sciences
Tel: +98(41)33364038
Fax: +98(41)33379420

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Received on Wed Mar 11 2020 - 04:30:03 PDT
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