Molecular Docking Server

Transition metals
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Author:  poonaminamdar [ Fri Aug 24, 2012 7:27 am ]
Post subject:  Transition metals

Well, related to metal-ligand docking.. I have come through a paper in which docking of vanadium ligands have been done for antidiabetic evaluation. I need vanadium parameter file which is essential for autodock, mainly.

I have been successful in calculating two of the parameter values from the equation, which is being depicted on the autodock website. I am facing problems in case of calculation of VdW well depth value of vanadium and it's solation parameter.

can anybody help me put regarding this?

Thanking you. :?: :)

Author:  hazaie [ Mon Aug 27, 2012 4:39 pm ]
Post subject:  Re: Transition metals


the fact is that it does not matter. Since vanadium is burried in the middle of the ligand it will not influence the docking at all. Simply use the parameters of another transition metal and there will be no difference.

Kind Regards,

Author:  poonaminamdar [ Tue Aug 28, 2012 5:31 am ]
Post subject:  Re: Transition metals

ok.. Thank u very much...

I have gone through a paper, in which authors have used Zn parameters for Ru metal.. If it is not making any difference, then we can use Zn parameters for the vanadium also, it seems. Can we?

Thanking you..


Author:  hazaie [ Wed Aug 29, 2012 1:27 pm ]
Post subject:  Re: Transition metals

Hi, yes you can.


Author:  poonaminamdar [ Thu Aug 30, 2012 4:34 am ]
Post subject:  Re: Transition metals


Thank u very much!

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