[Dock-fans] Model of lipid bilayer for docking

[Sudipto Mukherjee]

Francesco,

VMD can create MOL2 files. Save your membrane model as a MOL2 file; make sure it has charges. DOCK should work fine.
You can then use this MOL2 file to create a grid and spheres to proceed with docking. 
Singlepoint continuous scoring should also work, though Dock can take several minutes to score a receptor which includes a large membrane.

Docking does not do very well with large, non-druglike ligands. If your ligands have a lot of rotatable bonds, DOCK may face problems.
 
Regards
Sudipto Mukherjee
Graduate Student, Robert C. Rizzo Lab
Dept. of Applied Math & Statistics, Stony Brook University
Lab: 631-632-8519, Mobile: 631-220-5744


----- Original Message ----
From: Francesco Pietra <chiendarret at yahoo.com>
To: dock-fans <dock-fans at docking.org>
Sent: Friday, October 12, 2007 1:45:17 AM
Subject: [Dock-fans] Model of lipid bilayer for docking


I have raised a discussion on the tools available for building lipid
 bilayers.

In that context I suppose that phosphatidylcholine- or
polyenylphosphatidylcholine-based bilayers are computationally very
 costly.
Under the presumption that octane-water models of  lipid bilayer
 involve much
less computational cost, are they a promising initial route in the
 exploration
if there is any docking at all with complicated - non polymeric -
 potential
ligands? Also, are there examples of docking using more advanced models
 of
lipid bilayer?

Separately I have asked is complex bilayers built with VMD are
 transferable to
the Amber-Dock-Chimera world.

Thanks
francesco pietra 


       
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