FWIW, I have yet to see anyone get phosphate-containing compounds to work
with this model (e.g., nucleic acids). The phosphates themselves would
probably be even harder...
Good luck,
Jason
On Thu, Jun 29, 2017 at 1:15 PM, Michael Shokhen <michael.shokhen.biu.ac.il>
wrote:
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 29 2017 - 19:00:03 PDT
