AMBER Archive (2005)

Subject: AMBER: building monosaccharides with glycam force field

From: Lina Nilsson (linan_at_u.washington.edu)
Date: Tue Sep 20 2005 - 11:09:41 CDT

Dear all,
I am trying to build a simple monosaccharide - protein
(receptor-ligand) ystem using xleap (.prmtop, prmcrd). For the
methyl-terminated version of the monosaccharide this is no problem, I
just define the exocyclic OCH3 group of my sugar (adhered to the C1 of
the pyranose ring) as an OME/oxymethyl terminal group in glycam04. But
now I want to build the pyranose ring with only a 'terminal' hydroxyl
group at the C1 location. Does anyone know how to make this -OH addition
using glycam04?

Thanks,

Lina Nilsson
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