Trent E. Balius
tbalius at aol.com
Mon Jul 15 07:29:37 PDT 2013
Here is a good tutorial on running DOCK6.6:
Note that Sphere selector uses a mol2 file of a ligand usually to
select the spheres. The ligand usually defines a binding site on your
protien. If you are using multiple structures of the same protein it
might be advisable to align them it to the same frame. this can be
done with Chimera for example.
There are two separate task in docking:
the choice of sampling method and scoring method will effect your
You should use Anchor and grow method (sampling) and Grid score
I would suggest using the Tutorial above to guide you.
I would also suggest using the manual as a reference:
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: Mahesh Hegde <mahesh at biochem.iisc.ernet.in>
To: dock-fans <dock-fans at docking.org>
Sent: Mon, Jul 15, 2013 10:09 am
Subject: [Dock-fans] dock6.6
Hi, My name is Mahesh, i have started using Dock6.6 recently. I have
few problems and doubts as well, it might be basic for you people, so..
Some dms file (from same protein but different pdb files) are not able
make any clusters when i select sphere selectors, but some can form,
could be the reason?
I have one basic question, in dock6.6 there are 4 different types, amber
scoring and docking, anchor and grow docking, mpi docking, solvation
energy docking, so , on what preference i should select these programs?
and are these going to give different result?
Thank you very much for your time.
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