Re: [AMBER] standard parameter for sialic acid

From: David A Case <>
Date: Wed, 25 May 2016 20:02:39 -0400

On Wed, May 25, 2016, Bisignano, Paola wrote:

> Actually I realized that there should be standard parameters for the
> small molecule in the GLYCAM06. I downloaded the most recent version
> of parameters from the website and I went through the
> nomenclature to search for the sialic acid, which is supposed to be 0SA
> in the GLYCAM_06j-1.prep file.
> I do not know if I got the proper molecule, but actually I realized that
> the molecule is missing one -OH group, so the number of atoms are in
> fact 37, instead of 39.

For a stand-alone sialic acid, you need to link 0SA to ROH. More info is
given here:

(or in the glycam section of the Amber Reference Manual).

> p.s. I tried to send an email at but I did not get any answers

See this link for accessing the glycam mailing list:

However, Lachele regularly follows the Amber list, so you will probably get
a better answer from her soon.


AMBER mailing list
Received on Wed May 25 2016 - 17:30:02 PDT
Custom Search