[Dock-fans] Issues with dock6

Chris Fage cdfage at gmail.com
Mon May 9 01:24:34 PDT 2016

Hi Sudipto,

I entered the radii you suggested, then reran sphgen and sphere_selector.
However, the latter program still did not resolve after an overnight run.
When I performed docking in the past, I don't recall this stage taking so
long, and my CPU isn't exactly ancient (an Intel Core i7).

Also, I wouldn't qualify my ligand as small at 25 non-H atoms. But in the
past I was able to work with ligands of similar size in the software.

Any further suggestions are welcome.


On Sun, May 8, 2016 at 9:56 PM, Sudipto Mukherjee <sudmukh at yahoo.com> wrote:

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