[Dock-fans] question about sphgen and dock6

Trent E. Balius tbalius at aol.com
Mon Jul 8 07:54:03 PDT 2013


Hi gaojun,

Q1:
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.

Q2:
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:

http://ringo.ams.sunysb.edu/index.php/DOCK_Tutorials
http://ringo.ams.sunysb.edu/index.php/2013_DOCK_tutorial_with_Orotodine_Monophosphate_Decarboxylase

I hope this helps,

Trent

======================================
Trent E. Balius, PhD
Shoichet Lab – Faculty of Pharmacy,
University of Toronto
Office Phone: (416) 946-7304
Cell Phone: (516) 381-0926
URL: http://docking.org/~tbalius
======================================


---- 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



Hello dock-fans:
 
    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 
file?
 
    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 
right?
 
    Thanks to all dock-fans! 
 
 
2013-07-06
------------------------------------------------------------
gaojun

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