You can use Hex software (CUDA accelerated too) for protein-protein docking:
http://hex.loria.fr/
and than perform your MD.
Regards,
Filip
--- On Thu, 1/20/11, case <case.biomaps.rutgers.edu> wrote:
> From: case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] docking in AMBER for protein complex
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Thursday, January 20, 2011, 6:38 PM
> On Wed, Jan 19, 2011, Chinh Su Tran
> To wrote:
> >
> > I want to dock a complex of proteins (as a ligand) to
> another protein
> > (receptor). The tutorial using AMBER score in DOCK 6
> (
> > http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm)
> > just applies for small molecule as ligands (i.e drug)
> because it uses
> > Antechamber to generate the input file.
> > The Antechamber seems not to work for protein, I
> think, because it gave me
> > errors.
> >
> > Could anyone please give me some idea or links so I
> can figure it out?
>
> Dock is not really designed for protein-protein
> docking. You could ask on
> their mailing list (dock-fans) to see if anyone has tried
> it. But you will
> probably want to find code more suitable for that task.
>
> ...good luck...dac
>
>
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Received on Thu Jan 20 2011 - 11:00:02 PST
