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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 6:54 PM Bisignano, Paola <[log in to unmask]>
wrote:

>
> Dear GLYCAM users,
>
>
> I would like to simulate several galactose derivatives bound to a protein.
> I would like to proceed with a QM parametrization 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 portion 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,
>
>
>
> Paola
>
>
> Paola Bisignano, Ph.D.
> postdoctoral research associate
> Department of Pharmaceutical Chemistry
> Cardiovascular Research Institute
> University of California, San Francisco
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-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA