That might be because the hydroxyl pka for the isolated amino acid is 13,
so in most cases it won't be titratable. You might try just using a fixed
conformation pka prediction approach.
On May 7, 2015 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.
>
> Thank you,
> Michael
>
> *****************************
> Michael Shokhen, PhD
> Associate Professor
> Department of Chemistry
> Bar Ilan University,
> Ramat Gan, 52900
> Israel
> email: michael.shokhen.gmail.com
> email: shokhen.mail.biu.ac.il
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Received on Thu May 07 2015 - 04:30:04 PDT
