Der David,
many thanks for your advise.
I am studying now the R.E.D. article.
All the best,
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
________________________________
From: David Case <david.case.rutgers.edu>
Sent: Thursday, March 9, 2017 4:21:12 PM
To: AMBER Mailing List
Subject: Re: [AMBER] anionic Ser ?
On Thu, Mar 09, 2017, Michael Shokhen wrote:
>
> I have on my Linux server Amber16 and AmberTool16.
> I need to simulate by MD enzyme with deprotonated side
> residue oxygen atom (anionic OG atom) of catalytic Ser.
> The ff14SB force field used for the simulation
> has no parameters for such a case.
> What is the best way to resolve the problem?
The R.E.D. server might already have this residue, and in any event offers
a nice environment for generating force fields for modified residues.
A second alternative is to follow tutorial B5 to generate your modified amino
acid. Nothing is really easy, however, since the Lennard-Jones parameters
needed for a deprotonated hydroxyl oxygen might need to be tuned via quantum
calculations.
....dac
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Received on Thu Mar 09 2017 - 08:00:04 PST
