[gmx-users] charges

[Daan van Aalten]

Hi Corina

The PRODRG server usually comes up with sensible charges - and also a GMX
topology by the way. Try http://davapc1.bioch.dundee.ac.uk/prodrg

cheers

Daan

On Fri, 24 Oct 2003, CORINA BARBU wrote:

> Hello!
>
> It seems to me that the only place where charges are specified for atoms in a
> molecule is ff???.rtp file. Well, I have a molecule which is not a protein and
> for which I write the topology myself. I skip the step of using the pdb2gmx
> program in order to create a *.top file automatically. I guess I have to
> specify charges of the atoms in the molecule in a column next to that one with
> masses in the *.top(or *.itp)file ....
>
> So, I do not know where from to take the charges for the atom types I need for
> my molecule. I've seen some 0s in the ffG43a2nb.itp file. Plus, their sum
> should be 0(if I consider cgnr = 1 for all of them).
>
> What's the general procedure, how people deal with charges? For a
> instant I can take them from a ab initio calculation, but my molecule undergoes
> conformational changes over time and these charges should change...plus I have
> to apply electric field which makes them change even more. Is that enough for
> the ff if I provide a set of initial partial charges from ab initio calc?
>
> Somebody sure knows the answer! Thaks very much in advance!
> Corina
>
>
>
>


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Dr. Daan van Aalten                    Wellcome Trust CDA 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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