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. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users