On Fri, Apr 19, 2013, Jonathan Saboury wrote:
> My goal is to turn this PDB file (a non-standard organic molecule with
> Iron): http://pastebin.com/raw.php?i=G06ajgSw
> Into a prmtop and inpcrd file so that i can simulate it with OpenMM.
I don't have any help to offer. Just a note that you have chosen a really
hard problem. Amber doesn't offer much help for organometallic complexes, so
you might want to try to scour the literature to find out what others have
done with similar problems. You could consider tools like paramfit if you
could afford to do lots of quantum calculations. A lot will depend on what
you are planning to do with the simulation -- solvation properites, vibational
spectra, reactions, etc....
...dac
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Received on Sat Apr 20 2013 - 06:00:02 PDT
