Re: AMBER: building monosaccharides with glycam force field

From: <>
Date: Tue, 20 Sep 2005 15:12:33 -0400


     In order to terminate a sugar with a hydroxy group you must
create a hydroxy prep file. This prep file will contain the correct
atom types, connectivity, and RESP 0.010 partial atomic charges
determined at the HF/6-31G*//HF/6-31G* level of theory for the OH
group. Strictly speaking the hydroxy group should be determined
from an averaging of an ensemble of structures obtained from MD
simulations for several monosaccharides (ie. alpha and beta glucose,
galactose, mannose, GlcNAc). This is the method that was done in the
development of Glycam04 partial atomic charges. I believe the
appropriate parameters are included in Glycam04.dat for this type of

     However, it is "probably" okay to use the charges determined
from one or a handful of hydroxy-terminated monosaccharide
structure. Below is a prep file I generated a while ago for the C1
terminating hydroxy group for alpha glucose. (Notice that the sum of
the partial atomic charges are equal and opposite in sign to the sum
of the partial atomic charges of the terminal carbohydrate residues
in the Glycam04 prep file.)

     When you run your simulation and interpret the result, realize
that the OH partial atomic charges are approximate and we have not
tested hydroxy-terminate monosaccharides simulations. I would
recommend that you pay attention to the carbohydrate ring motion and
watch if it changes from one chair conformation to another (eg. 4C1,
1C4, etc.). If it does this may be an artifact of the calculation or
it may be real, so careful interpretation of the simulation will be

     To build the hydroxy-terminated monosaccharide using LEAP, you
will have to use the additional command "loadAmberPrep" to load the
hydroxy prep file printed below (the text in between the dashes)
[AMBER Manual Section 3.6.28]. Then create a new unit using the
command "sequence" [AMBER Manual Section 3.6.44] (eg. x = sequence
{OH 1GA} ). I hope this helps your endeavor.

0 0 2

hydroxy RESP 0.010 HF/6-31G*//HF/6-31G* (glucose)
1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0
2 DUMM DU M 1 0 -1 1.000 0.0 0.0 0.0
3 DUMM DU M 2 1 0 1.000 90.0 0.0 0.0
4 H HO M 3 2 1 1.000 90.0 180.0 0.430
5 O OH M 4 3 2 1.085 109.5 180.0 -0.624


Karl N. Kirschner, Ph.D.
Visiting Assistant Professor of Chemistry
Hamilton College, Clinton NY 13323

> 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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Received on Tue Sep 20 2005 - 20:53:02 PDT
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