simulations in amber are either constant pH or constant protonation.
default protonations are reasonable for the isolated amino acids, but
pka shifts may occur in proteins. it is possible to calculate pkas for
the initial structure, assign protonation states, and keep them. this
is ok as long as there are not conformation dependent pka changes that
cross your pH.
On 4/16/10, Andrew Voronkov <drugdesign.yandex.ru> wrote:
> Dear Amber users,
> when I am looking for questions about pH and Amber I get mostly information
> about constant pH simulations. But what pH is supposed to be by default,
> without constant pH simulations? Just neutral or what it depends from?
> As I understand in Amber pH is mostly set by protonation state of the
> molecules, so if not going to constant pH simulation I can approximately
> imitate some pH by setting corresponding protonation state distribution of
> amino acids. If physiological pH is required for protein simulation what can
> be general recommendation here - instant pH or default pH treatment?
>
> Sincerely yours,
> Andrew
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
===================================================================
Carlos L. Simmerling, Ph.D.
Professor, Department of Chemistry
CMM Bldg, Room G80 Phone: (631) 632-1336 Fax: 632-1555
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115 Web: http://www.simmerlinglab.org
===================================================================
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 16 2010 - 09:30:04 PDT
