Re: [AMBER] CpHMD for Ser residue?

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 7 May 2015 07:17:29 -0400

On Thu, May 7, 2015 at 6:39 AM, Michael Shokhen <michael.shokhen.biu.ac.il>
wrote:

> Dear Amber list members,
>
> I need to apply the amber CpHMD algorithm for pKa prediction and analysis
> of Ser residues in protein.
> What is a nickname of Ser used by this procedure and should I
> define any additional parameters for Ser there?
> Unfortunately I failed to find the answer in CpHMD tutorials
> as well as in the Amber15 user manual.
>

‚ÄčThat's because the serine residue has never been parametrized for use with
CpHMD. It has a pKa that is so high that it *very* rarely deprotonates
under physiological conditions (you can't even titrate arginine, which has
a lower pKa than serine).

There is a section in the Amber 14 manual that describes how you can
parametrize your own titratable residue if you need to.

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu May 07 2015 - 04:30:03 PDT
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