[Dock-fans] docking onto a planar surface

Ragothaman Yennamalli ragothaman at gmail.com
Thu Dec 29 11:50:46 PST 2011


Thanks Trent. This is very helpful. I will try this.
Raghu

On Wed, Dec 28, 2011 at 6:20 PM, Trent E. Balius <tbalius at aol.com> wrote:

> Hi Raghu,
>
> This sounds like macromolecular docking.  See the macromolecular docking
> section of the manual:
>
> http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#MacromolecularDocking
>
> Because a protein has so many atoms you will not want to do bipartite
> matching with all of the atoms and the active site spheres.  This may
> generate an intractable number of orients.  Instead use a ligand center
> file:
>
> use_ligand_spheres  yes.
>
> Therefore, you should generate two sets of spheres: one set on the polymer
> surface (receptor), and one set inside of the protein (ligand) surface.
>
> To do this you must run sphgen twice: Once using the parameter R, for
> receptor dms which will generate sphere outside of the surface and once
> using the parameter L for ligand dms which generates spheres inside the
> surface.
>
> See sphgen section:
> http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Sphgen
>
> See also
>
> http://mailman.docking.org/pipermail/dock-fans/2008-September/001719.html
>
> Because in Macromolecular docking two molecules with many internal degrees
> of freedom are used  it is likely  that all generated poses will contain
> clashes.
>
> So, you may need to turn off minimization and pruning.  After generating
> staring poses you will then need to come up with a relaxation schema.
>
> There are many other programs that specialize in protein-protein docking
> that may give you insight into this interesting area of research and help
> you relax your  generated complexes.
>
> I hope this helps,
>
>  Trent E. Balius
> Graduate Student, Rizzo Group,
> Department of Applied Mathematics and Statistics,
> Stony Brook University.
> Office: Math Tower 3-129, Phone: (631) 632-8519
> URL: http://www.ams.sunysb.edu/~tbalius/
>
>
>  -----Original Message-----
> From: Ragothaman Yennamalli <ragothaman at gmail.com>
> To: dock-fans <dock-fans at mailman.docking.org>
> Sent: Wed, Dec 28, 2011 3:56 pm
> Subject: [Dock-fans] docking onto a planar surface
>
>  Hi,
> Has anyone tried docking a protein onto a planar surface, such as the
> surface of a polymer? I am trying to do rigid docking of the protein onto
> the surface. In the first instance, I got an error message of "could not
> complete growth". With tweaking some parameters, the script completed
> running without any errors and also without any results written to the
> output mol2 file. Any ideas?
>
> Thanks and Regards,
> Raghu
>
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>
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