[Dock-fans] (no subject)

Gareth Williams 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?


Gareth Williams
Wolfson CARD
The Wolfson Wing
Hodgkin Building
Kings College London
London SE1 1UL
Tel:  020 7848 6806
Fax: 020 7848 6816

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