[Dock-fans] Issues with dock6

Chris Fage cdfage at gmail.com
Wed May 11 03:02:26 PDT 2016


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
>>>
>>> _______________________________________________
>>> Dock-fans mailing list
>>> Dock-fans at docking.org
>>> http://mailman.docking.org/mailman/listinfo/dock-fans
>>>
>>>
>>>
>>
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