[Dock-fans] dock6.6

Sudipto Mukherjee sudmukh at yahoo.com
Mon Jul 15 07:31:09 PDT 2013


Hi Mahesh,

For the docking spheres issue, can you make sure you are providing sphere selector with a ligand in the binding site? It may be helpful to visualize the dms surface and spheres generated (use showsphere) in chimera. Check to make sure there are actually spheres near your binding site before running sphere selector. 

As for the second question regarding which scoring function to select, the user manual explains each option in detail. You can use the DOCK tutorials listed at http://ringo.ams.sunysb.edu/index.php/DOCK_Tutorials as an example to get started. 
 
Regards
Sudipto Mukherjee, PhD
Dept. of Chemistry, Temple University
1901 N 13th St, Philadelphia, PA 19122


________________________________
 From: Mahesh Hegde <mahesh at biochem.iisc.ernet.in>
To: dock-fans at docking.org 
Sent: Monday, July 15, 2013 10:19 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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