Thanks for reply, I will definitely look to Pupil
Regards
vinod
On Fri, Feb 3, 2012 at 6:32 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> Hi Vinod.
>
> Marc basically itemized the issues.
>
> DFTB might actually have ruthenium parameters (they have Iron), but if
> you need spin changes for instance, then it is a big mess.
>
> Pupil is an otion, but it requires some expertise. There are tutorials
> available in the pupil download site.
>
> Amber 12 will have a native interface to a number of external QM
> programs, with the effort coming out of the San Diego people (Andy Goetz
> and Ross Walker). Amber 12 should be released maybe in March or April of
> this year.
>
> Adrian
>
>
> On 2/3/12 7:29 AM, Marc van der Kamp wrote:
> > Hi Vinod,
> >
> > I don't think there will be DFTB parameters for ruthenium any time soon
> > (but I could be wrong!). Ask the DFTB guys - i.e. Markus Elstner if you
> > want to know for sure and perhaps work on getting parameters, which would
> > be an extensive project.
> >
> > Interfacing AMBER11 with Gaussian may be a better option (but realize
> that
> > calculations will be slow, because you'll need methods - e.g. B3LYP -
> that
> > are much more expensive than semi-empirical ones).
> > Adrian Roitberg (or Ben Roberts?) may well chime in here, but they've
> > worked on making a Amber11/Gaussian interface using PUPIL, see
> > http://pupil.sourceforge.net and their paper:
> > A versatile AMBER-Gaussian QM/MM interface through
> > PUPIL.<http://www3.interscience.wiley.com/journal/117910767/abstract>
> > J.
> > Torras, G. M. Seabra, E. Deumens, S.B. Trickey and A.E. Roitberg. Journal
> > Computational Chemistry, 29, (2008) 1564-1573.
> >
> > --Marc
> >
> > On 3 February 2012 11:32, jani vinod<genomejani.gmail.com> wrote:
> >
> >> Dear all,
> >> I want to carry out protein ligand QM/MM simulation. My ligand is
> Ruthenium
> >> metal complex. In order to treat ruthenium i was using DFTB qmm method
> as
> >> their are no dftb parameters available at dftb.org i am unable to run
> >> QM/MM
> >> simulations. I would be very thankful if someone can provide me dftb
> >> parameters for ruthenium .
> >>
> >> OR
> >> Is their any way that we can coupled Gaussian with AMBER 11 so that MM
> can
> >> be treated by amber and QM part by gaussian
> >>
> >>
> >> Thanks
> >> vinod
> >> _______________________________________________
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> --
> Dr. Adrian E. Roitberg
> Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu
>
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Received on Sun Feb 05 2012 - 04:00:02 PST
