[gmx-users] How to fit ligand in specific site in protein in simulation

[sai nitin]

Hi gontchar,

I have done docking analysis using autodock using that ligand and binding
site but i want to do molecular dynamics (MD) using gromacs of same ligand
and binding site of my protein. Thats why i want to know how to place
ligand in specific binding site and run MD using gromacs.

Thanks,
Nitin

On Thu, Apr 12, 2012 at 10:34 AM, Андрей Гончар <gontchar at gmail.com> wrote:

> I think you have to use some special programm for this purpose.
> AutoDock, for example, will be the right choice.
>
> 2012/4/12 sai nitin <sainitin7 at gmail.com>:
> > Hi all,
> >
> > I am working on protein - ligand molecular dynamics simulation using
> > gromacs. I have a protein in which i know binding site which is composed
> of
> > 5 residues and i have one ligand i have to place this in binding site.
> >
> > Can any body tell me how to do place this ligand to binding site
> >
> > Thanks in advance
> >
> >
> > Cheers
> > --
> >
> > Sainitin D
> >
> >
> > --
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>
>
> --
>
> Андрей Гончар
> --
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-- 

Sainitin D
PhD student
Bioinformatics Group
Biotechnology Center
Technische Universität Dresden
Tatzberg 47/49
01307 Dresden, Germany
Tel Lab:+49 (0)351 463 40060
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