Many thanks everybody
for valuable and useful advises.
Now I am absolutely sure that
I won't go for constant pH MD
for this my task.
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: Adrian Roitberg <roitberg.ufl.edu>
Sent: Thursday, June 29, 2017 5:39:32 PM
To: AMBER Mailing List
Subject: Re: [AMBER] constant pH MD question
Hi Michael
This is VERY hard thing to do.
You need to create charge sets for all possible protonation states, and
create special residues that have fake protons. You then have to design
that residue as 'titratable' and compute the reference free energies of
protonation/deprotonation and fit them against experimental pKas.
This is not for the faint of heart!
I would recommend that you try to rebuild yourself the ASH residue as an
exercise, before you try to go into phosphates.
adrian
On 6/29/17 3:17 AM, Michael Shokhen wrote:
> Dear Amber experts,
>
> I have Amber16 and Amber Tools16.
> I need to simulate by constant pH MD complex of protein
> with ligands containing phosphonic and phosphate
> functional groups like structural examples presented in figure below.
> Unfortunately I didn’t find in amber documents and tutorials how to prepare
> for constant pH MD input files containing such functional groups.
> Your help highly appreciated.
>
> Thank you,
> Michael
>
> [cid:5878e43b-68e1-447c-9aa4-eb0655daf19e]
>
>
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Thu Jun 29 2017 - 10:30:03 PDT
