[Chimera-users] Out of topic for Elaine

Elaine Meng meng at cgl.ucsf.edu
Wed Sep 24 11:39:39 PDT 2008

Hi Francesco,
Although I did write the fortran code for "chemgrid" in DOCK 3.0,  
since that time it has been completely reimplemented by others in a  
different language.  I don't recall that program having anything to do  
with spheres - it just precalculates the scoring grid.  The spheres  
would be used later in the docking step.  If you are talking about the  
docking part, there are many other parameters unrelated to the scoring  
grid that control the length of the calculation.

Since I don't have any idea what is happening in your case, I suggest  
sending mail to the dock-fans list instead.  They would probably need  
to see your input file to know what parameters you used.
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 24, 2008, at 11:27 AM, Francesco Pietra wrote:

> Hi Elaine:
> Although out of topic, as the author of the program "grid" you could
> be in the best position to give me general advice.
> Selecting spheres for only a portion of the protein failed to execute
> "grid"  (at 0.3A grid_spacing) in a reasonable time. I choose this
> route in the hope to be able to examine docking (DOCK6) for the
> various parts of the molecule, in order to have the whole. I believe
> to have good reasons to do that.
> Is that what one should expect or does it mean that I did something  
> wrongly?
> Thanks
> francesco pietra
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