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

[Mark Abraham]

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