[Dock-fans] Issues with dock6

Chris Fage cdfage at gmail.com
Tue May 10 15:04:56 PDT 2016

Hello again,

Due to my troubles with sphere_selector, I manually picked the cluster
residing within my protein's binding pocket (this consists of 203 spheres).
After generating a box and grid, I was left with the statistics below.

Reading in grid box information.
Box center of mass                      :  -48.251   17.910  -38.082
Box dimensions                          :   39.901   35.575   46.777
Number of grid points per side [x y z]  :      135      120      157
Total number of grid points             :  2543400

The dock6 program crashed once again due to a segmentation fault. Is my
grid too complicated, perhaps?


On Mon, May 9, 2016 at 10:24 AM, Chris Fage <cdfage at gmail.com> wrote:

> 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.
> Regards,
> Chris
> 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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