[Dock-fans] Problem with sphere_selector

Pavan p.vaidyanathan at umiami.edu
Wed May 17 10:08:53 PDT 2006

Hello all,

I am running Dock 5.4.0 on a Mac Powerbook G4. I successfully
installed dock and ran the demo as well, so I know Dock is fine on my

I have been trying to dock a substrate ligand into my protein. I
created the charged MOL2 files for both protein and substrate using
Chimera. The MOL2 files look ok (similar to the ones in the demo). I
ran sphgen and created the list of sphere clusters for my protein.
Now, however, when I try to run sphere_selector as follows:

sphere_selector rec_all_clusters.sph lig_charge.mol2 6.0

the program immediately quits and creates an empty
selected_spheres.sph file, which says:

cluster     1   number of spheres in cluster     0

rec_all_clusters.sph contains 25 clusters ranging between 1 -24 and
then finally at the end of the 24th cluster, also has a cluster 0 with
the largest number of spheres in the cluster. I do not know if this is
why sphere_selector gets confused.

I could follow option 2 (in the dock manual) and choose a cluster
myself and put it into selected_spheres.sph and proceed. Except that I
did that already and could generate the grid.nrg files but got stuck
at docking where the program basically hung (for greater than 2 days
on a pretty fast mac laptop). The last line in dock.out was "reading
the energy grid from grid.nrg". Im guessing that I did something wrong
much before generation of the grid, which is why Im redoing everything
from the beginning.

If anybody has any pointers, I would be much grateful.  I have
attached the INSPH contents below. If any other information that you
might find helpful in the diagnosis is missing, please do tell.


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