[Dock-fans] stereo clash

Terry Lang terry at cgl.ucsf.edu
Mon Oct 3 11:52:43 PDT 2005

Dear Ricardo,
          The answer to your question is:  It depends on the parameters 
you have set.  For the problem you are seeing, I would recommend double 
checking two things.  First, you should make sure you have the 
"atom_model = all" set.  The alternative, united, will use a united atom 
model for scoring, which may leave the hydrogen radius too small for 
your situation.  Second, make sure you have the "use_internal_energy= 
yes" and the "use_clash_overlap = no"  Both parameters attempt to stop 
internal clashes during flexible ligand docking.  The internal_energy 
function is a bit more sophisticated and seems to work better in 
problematic cases.  If you are still having problems, please let me know.


Ricardo Nicoluci wrote:

> Hi,
> I applied the bug fixes and now Dock is performing well...I run it and 
> get values that are between -6 and -57...but, analysing the best 
> ranked molecules, the second one was in such conformation that one 
> hydrogen is just 1 A far away from another hydrogen in the same 
> molecule. A image of such conformation is attached. I was wondering 
> how Dock deals with hydrogen, do dock consider hydrogens during 
> docking or just the atoms bonded to it ?!
> Terry in a later email say that I could change the sphere box to pick 
> up a few more spheres and give a little more of flexibilty to get some 
> diferent conformations.
> -- 
> Ricardo de Paula Nicoluci
> PhD Student
> Medicinal Chemistry Laboratory
> IFSC - University of Sao Paulo
> Sao Carlos - SP - Brazil
> ------------------------------------------------------------------------
>Dock-fans mailing list
>Dock-fans at docking.org

P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986


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