[Dock-fans] Issues with dock6

Chris Fage cdfage at gmail.com
Wed May 11 10:10:08 PDT 2016


Hi Trent,

Ah, another embarrassingly silly mistake. I will pay closer attention in
the future. Thanks for your help!

Regards,
Chris

On Wed, May 11, 2016 at 5:13 PM, Trent E. Balius <tbalius at aol.com> wrote:

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