[gmx-users] How do you compute drug partial charges?

[Daan van Aalten]

Dear Yiannis

The PRODRG sever
http://davapc1.bioch.dundee.ac.uk/programs/prodrg/prodrg.html

will do this for you.
You can build your model from scratch using line-like drawings with a
simple text editor (see bottom of this E-mail for an example).
The program provides partial charges for most chemical groups.

If you want it to do metal ions, however, you have to fool the program a
bit by using a P atom instead and then changing the details in the GMX
topology generated by PRODRG.

cheers

Daan

On Mon, 22 Oct 2001 nicolis at guideo.fr wrote:

> 
> Hello,
> We are planning to model drug/metal cation interactions.
> What do you use to build your model molecule and to compute partial 
> charges to include in the topology file?
> Some years ago, I used to use Tripos Sybyl, which included Gasteiger, 
> Marsili and Huckel algorithms for partial charge computation.
> What are the free alternatives? Any suggestions?
> Thank you,
> Yiannis
> 
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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 

        O     C           O     C         Visit the PRODRG server to take 
        "     |           "     |         the stress out of your topologies!
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     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
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