[Dock-fans] Issues with dock6

Trent E. Balius tbalius at aol.com
Wed May 11 08:13:16 PDT 2016


 Hi Chris,

The ligand file needs to be a mol2 file, not a pdb file.  

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#SphereSelector
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm

Take care,

Trent

 

======================================
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: Trent E. Balius <tbalius at aol.com>
Cc: Sudipto Mukherjee <sudmukh at yahoo.com>; dock-fans <dock-fans at docking.org>
Sent: Wed, May 11, 2016 3:02 am
Subject: Re: [Dock-fans] Issues with dock6



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.dms
R
X
0.0
4.0
1.4
receptor.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. 


Regards,
Chris



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


======================================
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?



Regards,
Chris



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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