As a totally random aside, thank you for providing the facilities you do.
I work with oligosaccharides, and your group's website is valuable.
~Aron
On Sat, Dec 15, 2012 at 10:01 PM, Lachele Foley (Lists)
<lf.list.gmail.com>wrote:
> We don't have structural and charge information for muramic acid. I'm
> not aware that anyone in the group is working on it either. Our
> parameters should work, but you would need to develop charges.
>
>
> On Sat, Dec 15, 2012 at 5:16 PM, Aron Broom <broomsday.gmail.com> wrote:
> > Have you considered using the Glycan builder by the group that makes the
> > AMBER Glycam forcefield (Woods group)?
> >
> > You can find their main website here http://glycam.ccrc.uga.edu/ccrc/
> >
> > Follow the amber utilities or somesuch and then carbohydrate builder or
> > something. This will allow you to not only generate a PDB easily, but
> all
> > the residues will have the appropriate names.
> >
> > ~Aron
> >
> > On Sat, Dec 15, 2012 at 3:25 PM, Krisztina Feher
> > <feher_krisztina.yahoo.com>wrote:
> >
> >>
> >>
> >>
> >>
> >>
> >>
> >> Dear All,
> >>
> >>
> >>
> >>
> >>
> >> I am trying to generate a disaccharide consisting
> >> bGlcpNAc[1,4]aGlcpNAc[3-]-lactic acid in leap, see in the attched pdb
> file.
> >> Could someone suggest me the monosaccharide units I should use for
> >> this molecule? My own attempt from 4 residues ROH 1, WYB 2, 1YB 3 and
> >> a self-constructed LAC 4 residue has incorrect connections, please, see
> >> the screenshot of molecule in the editor.
> >>
> >> GlcpNAc[3-]-lactic acid is in fact muramic
> >> acid, but I did not see separate PDB code for in the GLYCMA06.prep
> >> file, so I made it from GlcpNAc and a lib file for lactic acid in
> >> antechamber with gaff atomtypes. Is there a better way for muramic acid?
> >>
> >>
> >>
> >>
> >>
> >>
> >> Thanks in advance,
> >>
> >> Krisztina
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
> >
> > --
> > Aron Broom M.Sc
> > PhD Student
> > Department of Chemistry
> > University of Waterloo
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Sat Dec 15 2012 - 23:00:02 PST
