[Dock-fans] stereo clash

Terry Lang terry at cgl.ucsf.edu
Thu Oct 6 20:08:00 PDT 2005


Dear Ricardo,

       I am still not clear what exactly you are doing.  Are you docking 
using Gold and then rescoring using DOCK or are you filtering the 
library using Gold and then redocking using DOCK or something else?  For 
the first question, there are several reasons why you could get that 
answer, most of which have to do with the parameters for 
anchor-and-grow.  If you send me your input file, I can try to give you 
some insight.  For the second question, once the growth is complete, the 
score that is reported is solely based on the ligand-receptor 
interaction and does not consider the internal energy of the ligand.

Sincerely,
Terry


Ricardo Nicoluci wrote:

> Hi,
>
> All these parameters were set to the way you said when I run Dock.
> There are two issues: First, how I could get such conformation and 
> second, even with that conformation, how could I get a low energy 
> value from that?
> The molecules that I used into Dock, are the results from the program 
> Gold. In other words, I am re-ranking the 200 best molecules that I 
> got from Gold using now the program Dock.
>
> Thanks,
> Ricardo.
>
>
> On 10/3/05, *Terry Lang* <terry at cgl.ucsf.edu 
> <mailto:terry at cgl.ucsf.edu>> wrote:
>
>     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.
>
>     Sincerely,
>     Terry
>
>
>     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
>     >
>     ------------------------------------------------------------------------
>
>     >
>     >------------------------------------------------------------------------
>     >
>     >_______________________________________________
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>     >
>     >
>
>     --
>     P. Therese Lang
>     Kuntz and James Labs
>     UCSF--Chemistry and Chemical Biology
>     Phone: (415)476-3986
>
>
>
>
>
>
>
> -- 
> Ricardo de Paula Nicoluci
> PhD Student
> Medicinal Chemistry Laboratory
> IFSC - University of Sao Paulo
> Sao Carlos - SP - Brazil 


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

 





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