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 glycam.org 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:
http://glycam.org/docs/forcefield/glycam-naming-2/
(or in the glycam section of the Amber Reference Manual).
> p.s. I tried to send an email at glycam.gmail.com but I did not get any answers
See this link for accessing the glycam mailing list:
http://glycam.org/docs/news/2015/05/14/a-mailing-list-for-glycam/
However, Lachele regularly follows the Amber list, so you will probably get
a better answer from her soon.
....dac
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Received on Wed May 25 2016 - 17:30:02 PDT
