Re: [AMBER] how is pH treated in Amber - other than constant pH simulations

From: Carlos Simmerling <>
Date: Fri, 16 Apr 2010 12:10:42 -0400

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 <> 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

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:
Stony Brook, NY 11794-5115 Web:
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Received on Fri Apr 16 2010 - 09:30:04 PDT
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