[Dock-fans] stereo clash

Ricardo Nicoluci nicoluci at gmail.com
Tue Oct 4 07:42:13 PDT 2005


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> 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
> > ------------------------------------------------------------------------
> >
> >------------------------------------------------------------------------
> >
> >_______________________________________________
> >Dock-fans mailing list
> >Dock-fans at docking.org
> >http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> >
> >
>
> --
> 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
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