Re: [AMBER] docking in AMBER for protein complex

From: Guillermo Mulliert Carlín <>
Date: Fri, 21 Jan 2011 09:24:47 +0100 (CET)


On Thu, 20 Jan 2011, case wrote:

|> 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 (
|> >
|> > 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.

        I am not a dock-fan, but some time ago I used molfit to do
protein-protein docking
        the resuts seemed correct, I am waiting for some experimental
validation of the model.
        To use the pdb output of molfit, I simply load them with tleap.

                                                Hope this help

                                                Guillermo Mulliert

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Received on Fri Jan 21 2011 - 00:30:04 PST
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