Subject: Re: CCL:help about partial charge

From: wzhuang/at/uci.edu
Date: Tue, 24 Feb 2004 07:44:51 -0800

Dear Marcel:

Thanks for the prompt reply.

can you give a comment about the partial charges from other force 
fields,like charmm and gromos?

also,what if I use the mullikan charges?

Wei

Dear Wei,

indeed if you are working on proteins, AMBER should give consistent
results, as the

atomic charges are Restrained ElectroStatic Potential derived charges
(RESP).

If the charges are all you need, and your systems contains only
already parameterized subsystems,

e.g. amino acid residues, the AMBER charges are a good choice.

On Monday, Feb 23, 2004, at 17:58 Europe/Amsterdam, wei wrote:

<excerpt>Dear All:

this is a vague question. I want to use gaussian to calculate the
frequency of the amide I mode (CO stretching) of one residue in a
small protein. and I want to treat the bath ( the left

part of the protein and the solvent ) as partail charge distribution.
now I need to decide how to determine the partial charges. The easiest
choice,of course,is to use the parameters

<excerpt>from the force field. but then the problem comes that which
force field should I choose.I got the impression that Amber is
extremely good at this because the determination of amber partial

</excerpt>charges are based on reproducing the electrostatic potential
in the space,while other force field is not. I don't know if this
impression is correct. can anybody give me some comments

or refer me to some papers? Also, what are other methods of
determining the partial charges ? ( I heard that mullikan is not very
good, although I don't know why )

All the Best 

Wei Zhuang

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</excerpt><fontfamily><param>Helvetica</param>–––––––––––––––––––––––––––––––––––––

<bold>dr. Marcel Swart

</bold>

Organische en Anorganische Chemie

Faculteit der Exacte Wetenschappen

Vrije Universiteit Amsterdam

De Boelelaan 1081

1081 HV Amsterdam

The Netherlands

F   +31-(0)20-4447488

E   swart/at/chem.vu.nl

W  http://go.to/m.swart

–––––––––––––––––––––––––––––––––––––</fontfamily>

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From: FyD <fyd-.at.-u-picardie.fr>
Date: Tue, 24 Feb 2004 22:15:48 +0100 (CET)

Concerning the derivation of RESP and ESP charges for AMBER force fields. You
can use our program RED http://www.u-picardie.fr/labo/lbpd/RED/. All is done
automatically and a tutorial is available in the RED manual...

Regards, Francois

>>e.g. amino acid residues, the AMBER charges are a good choice.

F.-Y. Dupradeau
 --
The Scripps Research Institute, San Diego, CA
Faculte de Pharmacie, UPJV, Amiens, France
 --
http://www.u-picardie.fr/labo/lbpd/fyd.htm