[Dock-fans] Dock 6 error

Brian Fochtman brianfochtman at gmail.com
Mon Dec 26 15:21:52 PST 2016


Cool. Glad it's working.

On Dec 26, 2016 6:18 PM, "Sacco, Michael" <michaelsacco at health.usf.edu>
wrote:

> Brian,
>
> Wow, thank you,I can't believe I missed that. Funny how we can look so
> deeply for the cause of a problem and it's often right in front of us.
> Anyways, thanks again, my docking can now proceed as planned.
>
> Best,
> Michael
> ------------------------------
> *From:* Brian Fochtman <brianfochtman at gmail.com>
> *Sent:* Monday, December 26, 2016 2:59:57 PM
> *To:* Sacco, Michael
> *Subject:* Re: Dock 6 error
>
> Hi Michael,
>      Has anyone reached out to you yet? It looks like your rec_box just
> contains your selected spheres but that you are docking using another set
> of spheres rec.sph, some of which probably fall outside of the rec_box.  Is
> there a reason you aren't docking with seleted_spheres.sph?
>      -Brian
>
> On Wed, Dec 21, 2016 at 4:20 PM, Sacco, Michael <
> michaelsacco at health.usf.edu> wrote:
>
>> Mr. Fochtman,
>>
>>
>> My name is Michael Sacco and I am a PhD student in the Chen lab at the
>> University of South Florida College of Medicine. I'm currently
>> encountering a problem with Dock 6.6 that I cannot resolve. I have spent a
>> long time troubleshooting, yet I cannot figure out what is wrong. After
>> submitting the dock6 command, I am receiving the following error message:
>>
>>
>> "Elapsed time:  0 seconds
>>
>> ERROR:  Could not complete growth.
>>          Confirm that the grid box is large enough to contain the ligand,
>>          and try increasing max_orientations.
>>
>>
>> 1 Molecules Processed
>> Total elapsed time:     0 seconds"
>>
>> I have tried changing the maximum number of orientations, set orient
>> ligand to "off", as well as followed the instructions that were offered
>> online, all to no avail. Additionally, I tried docking a very small
>> molecule and that did not fit either. My spheres are correctly placed, the
>> box is of sufficient size, and the docking has been previously performed
>> with Dock 3.5. I have attached my grid parameters, flexible docking input,
>> receptor file, crystallized ligand, sphere file, and box file. I was
>> wondering if you could take a look and let me know what you think? Any help
>> would be greatly appreciated.
>>
>> Thanks a lot,
>>
>> Michael Sacco
>>
>>
>
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