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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