[Dock-fans] SPHGEN problem

Michael Accardi Michael.Accardi at uoit.ca
Fri May 21 12:58:38 PDT 2010


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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