On Fri, Apr 10, 2015 at 3:08 AM, Alain Chaumont <chaumont.unistra.fr> wrote:
> Dear all,
> I am currently looking for force field parameters (in particular atomic
> charges) for mono amino acids at acidic conditions (pH < 2) and basic
> conditions (pH > 12).
> Is there a way to add a -COOH to an amino acid instead of COO-? I have
> also been looking in the literature however I have found none. But maybe I
> am missing something here.
> Has someone an idea where I could find such parameters. Or is it best to
> develop my own?
>
If you are talking about the side-chain protonation states (like for ASP
or GLU), then Gerald has told you how to do that.
If you mean that you want a C-terminal carboxylic acid instead of a
carboxylate, then these parameters do not exist in standard Amber
libraries. You can check the RED database (
http://q4md-forcefieldtools.org/)
to see if someone else has done that before. But you may wind up having to
derive your own charges (parameters you may be able to take from Amber).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Apr 10 2015 - 03:30:03 PDT
