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:
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> Dear All,
>
>
>
>
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> 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?
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> Thanks in advance,
>
> Krisztina
> _______________________________________________
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>
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Sat Dec 15 2012 - 14:30:01 PST
