[AMBER] standard parameter for sialic acid

From: Bisignano, Paola <Paola.Bisignano.ucsf.edu>
Date: Wed, 25 May 2016 23:43:53 +0000


I am running MD simulations with NAMD and amber most recent force field.
I parametrized my small molecule, a sialic acid or N-acetylneuraminic acid<https://en.wikipedia.org/wiki/N-acetylneuraminic_acid> (Neu5Ac) using Gaussian (to optimize the geometry and compute the ESP potential) and antechamber to fit the resp charges into the electrostatic potential obtained with Gaussian

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.

Did I make a mistake in the interpretation of the nomenclature? which is the sialic acid three letter code? I actually was unable to find any molecule with 39 atoms (so 42 including the first three dummy atoms).


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

Paola Bisignano, Ph.D.
postdoctoral research associate
Department of Pharmaceutical Sciences
Cardiovascular Research Institute, University of California, San Francisco
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Received on Wed May 25 2016 - 17:00:03 PDT
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