AMBER Archive (2006)

Subject: RE: AMBER: partial charge glycam

From: FyD (fyd_at_u-picardie.fr)
Date: Wed Jan 25 2006 - 03:23:06 CST

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

> 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.

The GLYCAM developers can correct me, but I am not sure the two strategies
reported are so different than that, or in any cases they present many common
points: CHELPG algo., HF/6-31G* theory level, single RESP stage with a
hyperbolic restraint qwt=.01, C-H charges = zero. This has to be opposed for
instance by what is used in AMBER FF development (Connolloy surface algo.,
HF/6-31G* theory level, two RESP stages with different hyperbolic restraints
(qwt=.0005/.001). Now, the two strategies might differ in the minimum selection
scheme and/or in the fitting procedure.

For instance, if we look @ the RNA project F-55: The project summary is
available in R.E.DD.B. @
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-55/info.html:
- Concerning the minimum selection, we simply selected a single conformation
(C3'endo since this is RNA) avoiding hydrogen bonds (HB) between the C'2 & C3'
hydroxyls (avoiding also the TS structures generated by the use of QM
constraints) and controlling mol. orientations using a rigid-body
re-orientation algo. HB affect charge values and the polarization obtained
using HF/6-31G* and, HB in sugars are problematic since a hydroxyl (O or OH)
can either be an acceptor or a donor of HB...
- Concerning the fitting procedure, we used charge constraints for C-H hydrogens
to set their charge values to zero. Other strategies are always possible.
Personnally, what I learnt is that fitting is neither averaging nor suming and
looking at the RRMS is a/one rigorous attempt for checking the quality of the
fit (a minimum number of charge constraints being always used since constraints
slightly increase the RRMS); The charge values reflecting only the MEP...
- Concerning the connections betwen sugars, once again by looking at the RRMS
and comparing the values obtained with and without intra or inter-molecular
charge constraints (possibly needed for the connections) is _one_ rigorous way
for answering 'YES' or 'NO' the constraints break or not your system. I
personnally prefer this type of approach compared for instance to some 'manual
manipulations'...
- Other differences ? May-be, I do not know ;-)

These emails demonstrates that different strategies are used in the charge
derivation even for a same FF. My opinion about answering to the question
"which one is the best" is not easy since charge values are affected by many
parameters and consequently many different options can be chosen. It is why we
developed the RESP ESP charge DDatabase where highly reproducible RESP and ESP
charges are available. R.E.DD.B. stores charge values, but also the
_computational conditions_ [mol. conformation (Cart. coordinates) and
orientation, basis set, MEP algo, fitting procedure, human errors, etc...] used
in the charge derivation procedure. Thus every modeler can use the charge values
available but also re-calculate, compare, criticize the values available; The
goal being to improve the procedures reported and try to answer which one(s)
is(are) the more suitable for protein, nucleic acid and/or sugars.

Exemple of comparisons are already available @
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-51/info.html
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-52/info.html
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-53/info.html
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-54/info.html
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-55/info.html
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-56/info.html for RNA

http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-45/info.html
up to http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-50/info.html for DNA

http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-1/info.html
up to http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-22/info.html for amino-acid
fragments.

http://www.u-picardie.fr/labo/lbpd/REDDB/up/W-46/info.html
up to http://www.u-picardie.fr/labo/lbpd/REDDB/up/W-50/info.html for solvent
molecules.

We hope the community will help to develop R.E.DD.B. and criticize what is
already available...

Regards, Francois

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