[Dock-fans] grid parallelization?

Francesco Pietra chiendarret at yahoo.com
Tue Nov 13 10:10:32 PST 2007


I wonder whether the calculation of grid is suitable to parallelization in a
future version of DOCK.

Using Magis' sphgen_cpp I can treat a whole pore protein model. I recognized
today that I has spheres for only a portion of the protein. Therefore, using
Magis' sphere_select, I have now selected a radius around a central atom within
the pore (the oxygen of a "natural" HOH residue). Because I am exploring
without previous knowledge where the ligand prefers to dock, I am creating a
grid for a box measuring 66 66 66 A for a total of more than 10 millions
points. In 30 min 10% of protein atoms processed. All processors, except one
(100%) are dormant.

That of having a point of symmetry is another problem. Luckily I had that
oxygen of WAT residue in the receptor noH.pdb file.

Thanks
frabcesco pietra


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