Re: [AMBER] System preparation for

Date: Tue, 3 Nov 2020 11:23:40 +0530


Thanks a lot. If you don't mind, I am asking a different scenario with two
protein chains bound to each other through a metal center zinc & I would
like to calculate the protein-protein interaction energy using,
then how should I proceed?

with regards,
Satyajit Khatua

---------- Forwarded message ---------
Message: 14
Date: Fri, 30 Oct 2020 08:07:32 -0700
From: Ray Luo <>
Subject: Re: [AMBER] System preparation for
To: AMBER Mailing List <>
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Yes indeed, you can leave the metal and the crystal water as part of
the receptor. Of course the ligand cannot be covalently bonded to the
receptor. Otherwise you don't have a case for calculating nonbonded
binding affinity by MMPBSA.

If you want to set up a metallo-protein system for MD and MMPBSA,
please refer to MCPB on how to do so.

All the best,
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Mon, Oct 26, 2020 at 9:31 PM SATYAJIT KHATUA
<> wrote:
> Dear Users,
> I am working on some ligand-bound metalloprotein systems. Following the
> tutorials and manuals from ambermd site, I understood that system
> preparation is a very important step here. Although there is a hint on how
> can be used for the case of the ligand-protein complex in
> I am wondering how can I implement this into my systems as they contain a
> catalytically important metal center at its active site (I think there is
> no tutorial about the system preparation of a ligand-bound
> It is very straight forward in the case of the complex. For the ligand, it
> is also not very hard to prepare the topologies. This leaves us only to
> parameterization of the protein system. Now as the metal center is
> important, I can't just strip it off from the protein, right? And another
> thing if there is any crystal water connected to that metal center to
> fulfill its coordination number, should I have to retain it for the case
> protein parameterization (talking about protein only, not the complex)?
> with regards,
> Satyajit Khatua
> _______________________________________________
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Received on Mon Nov 02 2020 - 22:00:02 PST
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