Re: [AMBER] Constant pH

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 31 Jan 2012 08:00:15 -0500

Sander cannot currently titrate termini, although that's on the list of things to do (at some point).

HTH,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Jan 31, 2012, at 7:26 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi everybody,
> 
> I'm dealing with a protein in which the C-terminal end forms a lid over the binding site. I has been proposed that this lid is acid labile and that at low pH it "uncovers" the binding pocket thus releasing the bound ligand.
> 
> My question is whether the constant pH in method in combination with conventional MD as implemented in Sander is appropriate to study whether this hypothesis is right?
> 
> I'm asking this before going into a wild goose chase. Any suggestions will be most welcome.
> 
> Many thanks in advance for any advice.
> 
> George
> 
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Received on Tue Jan 31 2012 - 05:30:02 PST