[Dock-fans] question about sphgen and dock6
Trent E. Balius
tbalius at aol.com
Mon Jul 8 07:54:03 PDT 2013
The spheres (sph file) are needed for docking specifically to orient
the ligand into the binding site.
The box file is used to generate the grids and the grids are used as
part of scoring ligands/conformations.
Docking calculation depends on the parameters chosen and the
flexibility of your ligand.
The following is a link to a good tutorial for running dock:
I hope this helps,
Trent E. Balius, PhD
Shoichet Lab – Faculty of Pharmacy,
University of Toronto
Office Phone: (416) 946-7304
Cell Phone: (516) 381-0926
---- Original Message ----
From: gaojun <gaojun at tongji.edu.cn>
To: dock-fans <dock-fans at docking.org>
Sent: Sat, Jul 6, 2013 10:06 am
Subject: [Dock-fans] question about sphgen and dock6
I am a new dock6 user, and I got a question recently.
I treated the atoms within the distance to 10A to a ligand as the
binding site, and produced the ms/sph files with dms/sphere_cpp
respectively. The box file is produced directly according to the
binding site, but not to the sph file. At the docking stage, a sph file
is need as one input parameter. My question is : the box file and
grid file are produced according to the binding site atoms, so the sph
file can be omitted? or clustering is not needed anymore for the sph
My second question is : On my server, for a protein and a small
molecular, sphgen_cpp runs very slow, but dock6 runs very fast. Is it
Thanks to all dock-fans!
Dock-fans mailing list
Dock-fans at docking.org
More information about the Dock-fans