Hello,
On Wed, Jan 27, 2010 at 6:11 PM, Tom Williams <dnaafm.gmail.com> wrote:
> Dear Ross,
>
> Thanks for your quick response to clarify this question!
>
> Could you give me one more suggestion?
> Does Amber provide any tool or command that can deprotonate / protonate a
> protein
> or peptide at certain pH ?
This is a tricky question... You can run constant pH molecular
dynamics in which the protonation state of each "titratable" residue
is changed according to a monte carlo criteria. Alternatively,
different protonated states of residues have different names (for
instance, ASP is an aspartate deprotonated, and ASH is an aspartic
acid with a proton, same for GLU and GLH). You would have to decide
whether you want to run constant pH simulations (this is described in
the manual), or whether you want to set the protonation states of each
of the acid/base groups. However, there's no way to set the pH and
have a program *figure out* what the appropriate protonation state
would be -- you'd actually have to run the constant pH MD.
Hope this helps,
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Jan 27 2010 - 16:00:02 PST
