[gmx-users] producing top and gro files for the molecule with metal ions.

[Tsjerk Wassenaar]

Hi Anna,

Interesting compound you have. In addition to the link sent by Mark,
I'd say that this compound is a bridge too far. It's a heavily
conjugated system with transitional metal. For parameterization you
should perform QM calculations, and because of the conjugation, you
can't really do it "in parts". So that's very expensive. The charge
from the Ru(II) can basically end up anywhere. The conjugation also
influences bonds, angles and dihedrals. Not something I would readily
want to burn my fingers on. Parameterization already is not for the
faint-hearted in more simple cases...

Cheers,

Tsjerk

On 6/26/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Anna Reymer wrote:
> > Hi!
> >
> > I am running GROMACS for DNA with Ruthenium (II) complex.  Please have
> > a look into pdb file below.
> > There is no parameters for any of transitional metals to produce
> > topology and coordinates for it. The Dundee PRODRG server
> > (http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ ) has parameters
> > only for C, N, O, S, P, H, F, Cl, Br, I the same situation is with
> > ANTECHAMBER (http://amber.scripps.edu/antechamber/antechamber.html).
> > Is it possible somehow to produce topology and coordinates files ?
>
> This is a difficult issue, and I think the advice here is sound
> http://wiki.gromacs.org/index.php/Parameterization
>
> Mark
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623