This definitely needs to go to the GLYCAM-L list. If you already did
that, I'll see it shortly.
On Fri, Oct 19, 2018 at 11:35 AM Bisignano, Paola <Paola.Bisignano.ucsf.edu>
wrote:
> 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?
>
>
>
> Thanks,
>
>
> Paola
>
>
> Paola Bisignano, Ph.D.
> postdoctoral research associate
> Department of Pharmaceutical Chemistry
> Cardiovascular Research Institute
> University of California, San Francisco
> ________________________________
> From: Lachele Foley <lf.list.gmail.com>
> 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 <david.case.rutgers.edu> 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
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Oct 25 2018 - 09:00:02 PDT
