AMBER Archive (2006)

Subject: RE: AMBER: partial charge glycam

From: Kevin Murphy (
Date: Tue Jan 24 2006 - 06:18:05 CST

Thanks for your helpful reply. I don't know if you read what Francois posted so I've cut out the most relevant paragraph
Now concerning, the connections of your new monosaccharide unit with others
belonging to GLYCAM: you simply have to use some linking fragments where you
will fix the total charge value for this fragment to a target value (usually
zero, but you can imagine any values...), i.e. a charge value which makes your
new unit compatible with other units (In this case just check the RRMS to see
if your constraint does not increase it too much). Concerning the linking
fragment itself I would first try the groupmnent OH or OMe... This type of
strategy is the more or less same for DNA, peptide or sugar; except that some
force fields use different 'tricks' and/or MEP algorithms...
This strategy is different to the one you've out lined below, I was wondering if you've tried it? is the charge on the glycosidic oxygen and surrounding atoms different? and does it matter? i.e. does it affect the dynamics of an oligosacchride chain during an MD simulation.


From: on behalf of
Sent: Fri 20/01/2006 15:39
Subject: Re: AMBER: partial charge glycam

Hi Kevin,

        We are currently working on the paper for publication. In short,
our charge fitting methodology is to a) generate a initial set of
partial atomic charges for a particular methyl glycoside (from an
RESP fitting on a selection of low energy QM optimized geometries).
The we perform a fully solvated MD simulation to obtain an ensemble
of conformations. We extract from this ensemble 100 conformations,
performed a partial geometry optimization (constraining the torsion
angles that freely rotated during the MD), and then performed another
RESP calculation. The monosaccharides that are linking other
monosacchrides have the hydrogen on the (to be) linkage oxygen
removed and their charges are summed into that oxygen, and then the
partial atomic charges on that oxygen are further adjusted to bring
the whole residue to a net charge of zero (unless it is a branched
carbohydrate, and then it is adjusted accordingly). The resulting
charge on the linkage oxygen has a reasonable value in comparison to
other ether oxygens. The only residues that have net charges (which
are non-integer) are terminal carbohydrates, branched carbohydrates,
and terminating groups (including NLN). As you mentioned most of
this is outlined in M. Basma, S. Sundara, D. Calgan, T. Vernalli,
and R.J. Woods J. Comput. Chem. 22 (2001) 1125-1137.

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

On Jan 20, 2006, at 6:28 AM, Kevin Murphy wrote:
> Hi,
> Does anyone know how the partial charges are re-calculated or
> adjusted for non terminal monosacchrides supplied with amber 8 for
> use with glycam or point me to a reference? I've read Dr Woods
> paper in J Comput. Chem 2001 on partial charge calculation for
> methyl glycosides but a lot of the monosacchrides supplied can be
> linked together to form oligosacchride chains and so don't have the
> methyl cap.
> Any help would be greatly appreciated
> Thanks
> Kevin Murphy

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