[AMBER] sugar derivatives parametrization

From: Bisignano, Paola <Paola.Bisignano.ucsf.edu>
Date: Wed, 17 Oct 2018 22:49:34 +0000

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 Bisignano, Ph.D.
postdoctoral research associate
Department of Pharmaceutical Chemistry
Cardiovascular Research Institute
University of California, San Francisco
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Received on Wed Oct 17 2018 - 16:00:02 PDT
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