[Dock-fans] Issues with dock6

Sudipto Mukherjee sudmukh at yahoo.com
Sun May 8 12:56:48 PDT 2016

Hi Chris,
Here is a sample sphgen input file:
rec.dms      #surface file generated above will be the input file
R            #flag to place spheres outside (R) or inside (L) of the surface 
X            #flag that informs sphgen of the subset of surface points to be used (X = all points)
0.0          #flag that prevent the generation of large spheres with close surface contacts(default= 0)
4.0          #maximum radius of the spheres generated (default = 4.0 Angstroms)
1.4          #minimum radius of the spheres generated (default = radius of probe)
rec.sph      #this will be the file which contained the clustered spheres generated Retain spheres between 1.4 and 4 angstroms. You don't need a large number of spheres in the active site. 
Use sphere selector with a small distance cutoff (3-5A) is fair for small ligands. This should run almost instantly - certainly not overnight.

    On Sunday, May 8, 2016 3:48 PM, Chris Fage <cdfage at gmail.com> wrote:

When I tried to generate spheres within a binding pocket, the pocket was only sparsely populated. Therefore, I altered the acceptable sphere radius 3.0-0.2. After this, I saw _many_ spheres. Wanting to exclude spheres far away from a manually placed ligand, I ran the sphere_selector routine. However, even after overnight, the program still appeared to be running and had not produced any output. 
Trying a different route, I created a subsection of residues lining the binding pocket, generated new spheres, and skipped the sphere selection phase. Unfortunately, when I ran dock6 the program crashed with the error:
Segmentation fault (core dumped)
I would be grateful for any insight and am happy to provide more details upon request.
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