[Dock-fans] dock6.6

Trent E. Balius tbalius at aol.com
Mon Jul 15 07:29:37 PDT 2013


Hi Mahesh,

Here is a good tutorial on running DOCK6.6:

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

Q1:
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.

Q2:
There are two separate task in docking:
(1) sampling:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#LigandFlexibility
(2) scoring:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Scoring
the choice of sampling method and scoring method will effect your 
results.
You should use Anchor and grow method (sampling) and Grid score 
(scoring).
I would suggest using the Tutorial above to guide you.
I would also suggest using the manual as a reference:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm

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: 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 
got
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 
to
make any clusters when  i select sphere selectors, but some can form, 
what
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.



--
Sincerely,
Mahesh Hegde

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