Re: [AMBER] Carboxyl and Carboxylate groups with GLYCAM

From: Lachele Foley <>
Date: Tue, 21 Oct 2014 13:44:32 -0400

Sorry to take so long responding.

You *could* do the R-COO- variant, but I'm not sure you should. You'd
definitely need to do some heavy validation. Our parameters are for
carboxylate groups attached to sugars, and there is no guarantee that
the parameters would be appropriate for such a different chemical
environment. For example, we can't use the NHCO parameters from a
peptide backbone for our X-NAc residues. Did you try using one of the
lipid force fields? The GLYCAM lipid force field is decent, but
treats only a few subunits, so you'll probably do better with one of
the other AMBER lipid ff's.

On Mon, Oct 20, 2014 at 11:52 AM, sa <> wrote:
> Hi
> I am wondering if it possible to use the GLYCAM force field model R-COOH
> and R-COO- groups (where R is a alkane chain)? If yes, which atom types
> should I use ?
> Thanks for your response
> SA
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Tue Oct 21 2014 - 11:00:04 PDT
Custom Search