[Dock-fans] SPHGEN problem

gongxingwen gongxingwen at 163.com
Sat May 22 08:43:45 PDT 2010


You should type the folowing
 
cd /your path/dock6/bin
./sphgen
 
and then it would work. In addition, sphgen can only handle no more than 9999 atoms. For large protein, sphgen_cpp is more suitable. 
 
Good luck.
Xing-Wen Gong 

> -----原始邮件-----
> 发件人: "Michael Accardi" <Michael.Accardi at uoit.ca>
> 发送时间: 2010年5月22日 星期六
> 收件人: "dock-fans at mailman.docking.org" <dock-fans at mailman.docking.org>
> 抄送: 
> 主题: Re: [Dock-fans] SPHGEN problem
> 
> 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
> >>
> >>
> >>
> >> _______________________________________________
> >> Dock-fans mailing list
> >> Dock-fans at mailman.docking.org
> >> http://mailman.docking.org/mailman/listinfo/dock-fans
> >>
> >>
> > _______________________________________________
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> >
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