[Dock-fans] SPHGEN problem

Michael Accardi Michael.Accardi at uoit.ca
Fri May 21 13:18:00 PDT 2010


Unfortunately I received the following message:

$/home/100262488/dock6/bin/sphgen INDOCK
open: No such file or directory
apparent state: unit 4 named DMSWT49BHo.dms
lately reading sequential formatted external IO
aborted (core dumped)

I also would like to mention that I did not find a file or .exe of anything called INDOCK in the bin folder although you mentioned it would exist in the directory I was in. Could this be the issue? And if so, where could one be found/created.

Additionally, I still only produce an OUTSPH file with nothing in it and a sphgen.exe.stackdump file. I ensure I delete these files before each time I try and run sphgen.

Thank you for your continued help John, 
Mike

-----Original Message-----
From: John Irwin [mailto:jir322 at gmail.com] 
Sent: Friday, May 21, 2010 4:09 PM
To: Michael Accardi
Cc: dock-fans at mailman.docking.org
Subject: Re: [Dock-fans] SPHGEN problem

how about

/path/to/sphgen INDOCK

(and an INDOCK file should exist in the directory where you are)

On Fri, May 21, 2010 at 12:58 PM, Michael Accardi
<Michael.Accardi at uoit.ca> wrote:
> Alright I see something different now. When I type the following (/home/100262488/dock6/bin/sphgen) I get this:
>
> $/home/100262488/dock6/bin/sphgen
> Open: No such file or directory
> Apparent state: unit 4 named DMSWT49BHo.dms
> Lately reading sequential formatted external IO
> Aborted (core dumped)
>
> I am incredibly new to this cygwin/unix language so this result is confusing.
>
> Does this clarify my issue?
>
> -----Original Message-----
> From: John Irwin [mailto:jir322 at gmail.com]
> Sent: Friday, May 21, 2010 3:41 PM
> To: Michael Accardi
> Cc: dock-fans at mailman.docking.org
> Subject: Re: [Dock-fans] SPHGEN problem
>
> did you try /full/path/to/sphgen
> ?
>
>
>
> On Fri, May 21, 2010 at 12:29 PM, Michael Accardi
> <Michael.Accardi at uoit.ca> wrote:
>> To whom this may concern,
>>
>>
>>
>> I recently installed DOCK 6.4. Unfortunately, when trying to dock a molecule
>> into my protein I cannot get past the sphgen step. I have installed DOCK
>> twice now, and I installed devel when I first installed cygwin.  I have
>> looked through the archives and although some people have had a similar
>> problem, no resolutions have worked for my situation.
>>
>>
>>
>> Unlike in the dock 6 tutorial, I cannot simply write sphgen to start the
>> program. When I do I receive this:
>>
>> bash: sphgen: command not found
>>
>>
>>
>> Instead, in order to get sphgen to 'work' I have to insert the following
>> command:
>>
>> run sphgen
>>
>>
>>
>> After sphgen I am supposed to get 2 output files (the OUTSPH and a .sph
>> file). However,  I only get a OUTSPH file which has nothing in it and a
>> sphgen.exe.stackdump file but NO .sph file.
>>
>>
>>
>> The sphgen.exe.stackdump contains the following:
>>
>>
>>
>> Stack trace:
>>
>> Frame     Function  Args
>>
>> 0023C3B8  7C802542  (000006C0, 0000EA60, 000000A4, 0023C4AC)
>>
>> 0023C4C8  610C2643  (00000000, 7C802600, 7C802542, 00000000)
>>
>> 0023C5A8  610BF2F7  (00000000, 00000000, 00000000, 00000000)
>>
>> 0023C5F8  610BF70B  (0000A9C8, 0023C620, FFFFFFDE, 00000006)
>>
>> 0023C6B8  610BF831  (0000A9C8, 00000006, 0023C6E8, 610BF8D5)
>>
>> 0023C6C8  610BF86C  (00000006, 0023CE80, 0023C6E8, 01A4CA18)
>>
>> 0023C6E8  610BF8D5  (00000006, 00000000, 00415C40, 00000000)
>>
>> 0023C708  004106EF  (00415C40, 00000001, 01A4C338, 00000190)
>>
>> 0023C858  0040A4AF  (00414080, 0023CC90, 00000050, 00000000)
>>
>> 0023CCF8  004010B1  (00405890, 01D019D0, 0023CD28, 004046A8)
>>
>> 0023CD28  004046D3  (00000001, 01D019D0, 01CD80E0, 00008000)
>>
>> 0023CD98  61006E73  (00000000, 0023CDD4, 61006720, 7FFDB000)
>>
>> End of stack trace
>>
>>
>>
>> Additionally in my INSPH file, which is not a .txt file, I have ensured that
>> the name of my .dms file (which I generated with Chimera's Write DMS tool)
>> is the same as the .dms file I placed in the same folder which contains the
>> sphgen.exe (This location is in my dock6/bin folder). Therefore, the
>> sphgen.exe, INSPH and .dms file are located in the same folder.
>>
>>
>>
>> Do you have any help or advice?
>>
>>
>>
>> Thanks in advance,
>>
>> Mike
>>
>>
>>
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>>
>>
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