Did you get this worked out?
If what you need is the acetyl derivative of a common sugar, then the
website should be able to build it for you and supply parameters.
If you want to use leap, then these instructions should help:
http://glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/
On Tue, Jul 2, 2019 at 2:03 PM ABEL Stephane <Stephane.ABEL.cea.fr> wrote:
>
> My bad !! so as suggested by Pr Case, you shoud use GLYCAM and for instance the webserver "glycam web" to obtain the parameters
>
> https://dev.glycam.org/
>
> Stéphane
>
> ________________________________________
> De : Kolattukudy P. Santo [santotheophys.gmail.com]
> Envoyé : mardi 2 juillet 2019 19:41
> À : AMBER Mailing List
> Objet : Re: [AMBER] R . E. D
>
> Hi Stephane
> There are pyruvates of saccharides such as Mannose Pyruvate, like ManAc
> Santo
>
> On Tue, 2 Jul 2019 at 13:28, ABEL Stephane <Stephane.ABEL.cea.fr> wrote:
>
> > hi,
> >
> > Pyruvates are not carbohydrates. So "I think" that you can use GAFF based
> > parameters and not GLYCAM suggested by Pr Case (you mentionned
> > carbohydrates in your first questions)
> >
> > Stéphane
> >
> > ________________________________________
> > De : Kolattukudy P. Santo [santotheophys.gmail.com]
> > Envoyé : mardi 2 juillet 2019 19:22
> > À : david.case.rutgers.edu; AMBER Mailing List
> > Objet : Re: [AMBER] R . E. D
> >
> > Thank you Prof. Case. In fact I had looked at this. But I didnot find
> > library for Pyruvates, ( derivatives of pyruvic acid) which I need to
> > simulate.
> > Santo
> >
> > On Tue, 2 Jul 2019 at 13:05, David A Case <david.case.rutgers.edu> wrote:
> >
> > > On Tue, Jul 02, 2019, Kolattukudy P. Santo wrote:
> > >
> > > >I am trying to calculate partial charges for polysacharides or MD
> > > >simulation.
> > >
> > > We recommend using the GLYCAM libraries to describe polysaccharides. See
> > > section 3.3 of the Reference Manual, or visit glycam.org.
> > >
> > > ....dac
> > >
> > >
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> > >
> >
> >
> > --
> > *Dr. K. P. Santo*
> > *Post doctoral Associate *
> > *Department of Chemical and Biochemical Engineering*
> > *Rutgers, The State University of New Jersey*
> > *New Brunswick, New jersey*
> > *USA*
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> > AMBER mailing list
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> *Dr. K. P. Santo*
> *Post doctoral Associate *
> *Department of Chemical and Biochemical Engineering*
> *Rutgers, The State University of New Jersey*
> *New Brunswick, New jersey*
> *USA*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Wed Aug 21 2019 - 13:00:02 PDT
