[Dock-fans] (no subject)
gareth.2.williams at kcl.ac.uk
Fri Sep 13 08:26:35 PDT 2002
I'm trying to run dock on a validation set of protein:compound crystals.
Starting with just one complex I take the protein pdb file and generate a
mol2 file with the openeye molcharge application (an empty line before the
atom records has to be deleted). I take the compound pdb file and do the
same (a SUBSTRUCUTE entry has to be added here). The box pdb file is such
that it encompasses the bound compound. I take 5 spheres per probe within
this box to generate a sph file.
I set up the grid.in and dock.in files as for the first run in the DOCK4.0
user manual and run GRID and DOCK. The DOCK calculation takes ~0.02 seconds
and the nrg file has the ligand 77 angstoms away from the protein target.
Any suggestions as to why the ligand is outside the box?
The Wolfson Wing
Kings College London
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