[gmx-users] A question about partial charges

[Daan van Aalten]

Hi Ioannis

It's always a good idea to run through PRODRG generated topologies and
check for things that you're not happy with. Hydrogens on nitrogens are a
problems - is not really trivial to automatically determine in
multi-cyclic aromatics with more than one N which one(s) should be
protonated.

In the stand alone version of PRODRG it is possible to delete/add
hydrogens, and this will soon also be available on the server so that
would solve part of your problem.

The PRODRG charges are derived from the GROMOS87 topology building block
file and are only a rough approximation.

cheers

Daan

On Thu, 11 Apr 2002 nicolis at guideo.fr wrote:

>
> Hello,
> I wonder if there is a compatibility issue about using Gasteiger and Marsili partial charges with the gmx forcefield.
> The reason is we want to simulate a molecule with ionised NH but the prodrg server don't take into account the hydrogen missing so we don't get the charge distibution we want. So we used the prodrg topology files, substituting the Gasteiger-Marsilii charges instead of the prodrg charges.
> It seems to work fine but I wanted to verify there is no problem on proceeding this way.
> Thank you,
> Ioannis
>
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##############################################################################

Dr. Daan van Aalten                    Wellcome Trust RCD Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

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