[Chimera-users] End graphical representation from Dock tutorials

Francesco Pietra chiendarret at yahoo.com
Mon Oct 8 02:34:05 PDT 2007

I carried out all Dock6.1 tutorials with the aid of Chimera 1.2422 and DMS. The
relevant files used for, and got from, the flexible-ligand docking tutorial are
attached. I believe I used defaults. The out file attached is the one of the
four out files (from mpirun -np 4 ....) that seems to me to be relevant.

How to view graphically the best scored ligand from flex_scored.mole2 in the
protein? Just combine flex_scored.mole2 with the ligand-deprived receptor?

This in view of my project of looking for docking between a family of
lypophilic natural products (conformationally studied in vacuum with Amber9
simulated annealing) and a complex, large protein. I.e., by carrying out a
process of the type illustrated by the docking tutorial for each pocket of the
protein. I know there is interaction between the two (though a mere
disassembling of the lipid bilayer can't be rigorously ruled out yet) but no
idea where.

francesco pietra

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