Re: [AMBER] sugar derivatives parametrization

From: Lachele Foley <>
Date: Thu, 18 Oct 2018 22:58:32 -0400

This question belongs a bit in both lists - AMBER and GLYCAM.

So, first the AMBER-level question: What is the amino acid to which you
want to attach the galactose? What are the types of galactose derivative?
It might be that the parameters you need already exist.

If you do need to develop the params, then we'll switch to the GLYCAM list
where you are likely to get a more detailed response.

On Wed, Oct 17, 2018 at 6:50 PM Bisignano, Paola <>

> Dear Amber user,
> I would like to simulate several galactose derivatives bound to a protein.
> I would like to procede with a QM parametrization of the entire molecule,
> by using gaussian to optimize the geometry and calculate the ESP and then
> use the AMBER tools to fit resp charges and generate the parameter sets for
> simulating with the AMBER ff.
> Shall I parametrize the entire molecule or just the aglycon and use the
> GLYCAM parameters for the galactose moiety? If the latter is the best
> option, how can I parametrize the aglycon with a 'reacting' end to be then
> attached to the standard galactose moiety?
> I tried to look if anybody asked the same question before, but I could not
> find any hints.
> Thanks for your time and help,
> p.s. should I have sent this email to the GLYCAM mailing list instead? If
> so, sorry to bug you
> Paola
> Paola Bisignano, Ph.D.
> postdoctoral research associate
> Department of Pharmaceutical Chemistry
> Cardiovascular Research Institute
> University of California, San Francisco
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Thu Oct 18 2018 - 20:00:02 PDT
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