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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 03 2012 - 05:30:03 PST
