Re: [AMBER] CpHMD for Ser residue?

From: Jason Swails <>
Date: Thu, 7 May 2015 07:17:29 -0400

On Thu, May 7, 2015 at 6:39 AM, Michael Shokhen <>

> 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.


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