Re: [AMBER] sugar derivatives parametrization

From: Bisignano, Paola <>
Date: Fri, 19 Oct 2018 15:34:14 +0000

Hi Lachele,

I simulated in the past the galactose and it looks good to me. I need to simulate sugar derivatives that have the galactose moiety bound to a substitute indole ring, one of the molecule is X-gal.

So I would like to get the parameters for the indole portion and use the standard parameters for the galactose moiety. Does this make sense? Or shall I just calculate the ESP with Gaussian of the X-gal?



Paola Bisignano, Ph.D.
postdoctoral research associate
Department of Pharmaceutical Chemistry
Cardiovascular Research Institute
University of California, San Francisco
From: Lachele Foley <>
Sent: Thursday, October 18, 2018 8:00:27 PM
To: AMBER Mailing List
Subject: Re: [AMBER] sugar derivatives parametrization

Yes... what Dave said. I didn't see that before sending my response. But,
that's the basic procedure: let's make sure you know how the existing stuff
works first.

On Thu, Oct 18, 2018 at 2:09 PM David Case <> wrote:

> On Wed, Oct 17, 2018, Bisignano, Paola wrote:
> >
> > 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.
> First step would be to make sure you are comfortable with how galacaose
> itself (and related molecules) are handled with GLYCAM.
> And yes: sending email to the glycam mailing list will probably get
> better and quicker answers. It's likely to be Lachele that answers this
> sort of question anyway.
> ...good luck....dac
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
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Received on Fri Oct 19 2018 - 09:00:02 PDT
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