Is your goal to only have amino acid side chains protonate and deprotonate?
If so, as Monsurat suggested, Jason's multiple constant pH tutorials are
the way to go constant pH is the way to go. Also check out his replica
exchange md tutorial: http://jswails.wikidot.com/ph-remd
Is your goal to have your non-covalently bound ligands protonate and
deprotonate as well? If that is the case, then I don't believe it will be
possible with constant pH and you might have to employ a different
technique like QM/MM.
On Thu, Jun 29, 2017 at 2:31 AM, Monsurat Lawal <lawalmonsurat635.gmail.com>
wrote:
> Hello Michael,
>
> Here is the link for tutorial by Jason Swails and T. Dwight McGee Jr.
> http://ambermd.org/tutorials/advanced/tutorial18/
>
> Best wishes,
> Monsurat.
>
> On Thu, Jun 29, 2017 at 11:17 AM, Michael Shokhen <
> michael.shokhen.biu.ac.il
> > 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
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Andrew Schaub
Graduate Program in Chemical & Structural Biology
Tsai Lab, http:///www.tsailabuci.com/ <http://www.tsailabuci.com/>
Luo Lab, http://rayl0.bio.uci.edu/html/
University of California, Irvine
Irvine, CA 92697-2280
949-824-8829 (lab)
949-877-9380 (cell)
aschaub@uci.edu <http://www.linkedin.com/pub/andrew-schaub/9a/907/382/>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 29 2017 - 07:00:02 PDT
