AMBER Archive (2008)

Subject: AMBER: Building O-Ac modified monosaccharides consistent with Glycam force field parameters

From: Francois Theillet (ftheille_at_pasteur.fr)
Date: Fri Nov 07 2008 - 09:24:36 CST

Dear all,

I want to add O-Ac on carbohydrate residues. I read the detailed help of
Karl Kischner http://archive.ambermd.org/200509/0150.html, and followed
the indications of the tutorial A1 (thank you to all of their authors).
The "fast and dirty method" would be the following : I have to determine
the partial atomic charges of the O-Ac in a Met-O-Ac molecule using
HF/6-31G*//HF/6-31G* RESP 0.010, and then replace correctly the charges
in the antechamber generated prep file.

However, I do not have any access to Gaussian softwares, and I tried to
use the free WebMO Demo server.
Unfortunately, jobs are limited to 60s on this shared resource, and the
optimization of geometry and partial charges calculation (using a
Gaussian engine) can be done at the HF/3-21G level of theory only (after
a first optimisation at the HF/STO-3G level of theory) (and the RESP
methodology is apparently not used for the charges calculation).

I know that Glycam force field parameters are done at the HF/6-31G*/
level of theory and that there is a risk that the partial charges using
another methodology are not consistent with Glycam parameters.

Thus, I would like to know what would you think if I used this basic
WebMO demo server output for modifying an antechamber geerated prep file
for the new residues (apart from the problem of the ensemble of
conformations).

(If we compare with the charge parameters of a GlcNAc for example, it
seems to me that the the Met-atomes (C and H) of the O-Ac are
excessively charged.)

I attached the ouput of the WebMO calculations.
I hope that my account and question are not too stupid...

I thank you in advance for your answers,

François Theillet.


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