[Dock-fans] docking onto a planar surface

Trent E. Balius tbalius at aol.com
Wed Dec 28 16:20:32 PST 2011

Hi Raghu,

This sounds like macromolecular docking.  See the macromolecular docking section of the manual:


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:

See also


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

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,

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Dock-fans at mailman.docking.org

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