Dear Krisztina,
You could split your disaccharide into two building blocks (BD); a
methyl-acetal and an acetal; use an inter-molecular charge constraint
(inter-mcc) between these two BD as it follows:
R.E.D. LEaP
2 building blocks 2 mol. fragments
R1O-Me HO-R2 ------> R1O + R2 ------> R1O-R2
<------> fragment fragment
inter-mcc = 0 generation association
The new version of R.E.D. perform atom typing as well as molecular
fragment association.
regards, Francois
> 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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Received on Sun Dec 16 2012 - 00:30:01 PST
