AMBER Archive (2006)

Subject: Re: AMBER: partial charge glycam

From: FyD (fyd_at_u-picardie.fr)
Date: Sat Jan 21 2006 - 01:30:37 CST

Quoting Kevin Murphy <k.murphy_at_hud.ac.uk>:

> 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.

You can see some examples in R.E.DD.B.:
http://www.u-picardie.fr/labo/lbpd/REDDB/
CHELPG; HF/6-31G*; 1-RESP-STAGE qwt=.01; H-C constraint set = 0.0

For instance: http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-49/info.html
or better http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-55/info.html
since for RNA/ribose you have intramolecular H-bonds...

To get the files (and RESP input), use the "Download section" and use the
project code "F-49" or "F-55" to retrieve the files (RESP inputs)...

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...

You can use several conformations (optimized by QM) in the fitting process and
also several orientations for each conformation if you wish. For that you can
use R.E.D.-II http://www.u-picardie.fr/labo/lbpd/RED/ were intra-molecular
charge constraint are not yet handled automatically. On the contrary, all is
done automatically in R.E.D.-III (available when the manual will be
written...).

regards, Francois

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