[Dock-fans] Issues with dock6

Sudipto Mukherjee sudmukh at yahoo.com
Wed May 11 04:52:51 PDT 2016

Hi Chris,
Could you post the dock input file that caused the crash? We would like to replicate the crash and try to eliminate it. 


On Wed, May 11, 2016 at 3:02 AM -0700, "Chris Fage" <cdfage at gmail.com> wrote:

Hi Sudipto and Trent,
I replaced my flex.in file for dock6 with a template that worked for me in the past, then changed the entries accordingly. Now, dock6 doesn't crash, so there must have been a problem with the input after all. Everything is looking good.
I am still curious, however, why the sphere_selector routine is hanging. I am using the INSPH parameters:receptor_noH.dmsRX0.04.01.4receptor.sph
I am entering the sphere_selector parameters as follows:/home/chris/dock6/bin/sphere_selector receptor.sph ligand_manual.pdb 5.0
As the name implies, ligand_manual.pdb contains coordinates for a ligand placed manually within the active site. 
On Wed, May 11, 2016 at 12:26 AM, Trent E. Balius <tbalius at aol.com> wrote:

 Hi Chris,

The sphere_selector script should run in seconds not hours.  

I suspect that there is an issue with one of your input files.   

When is DOCK producing the seg.fault?

Could you run dock with the -v flag, the output will tell you at what part of the docking procedure it is failing.  

I hope that this helps. 



Trent E. Balius, PhD

Postdoc, Shoichet Lab, 

Dept. Pharm. Chem., UCSF

Phone: (415) 514-4253

URL: http://docking.org/~tbalius




-----Original Message-----

From: Chris Fage <cdfage at gmail.com>

To: Sudipto Mukherjee <sudmukh at yahoo.com>

Cc: dock-fans <dock-fans at docking.org>

Sent: Tue, May 10, 2016 3:05 pm

Subject: Re: [Dock-fans] Issues with dock6

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.



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.





 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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