[Dock-fans] Dock-fans Digest, Vol 85, Issue 15

Prashant Kumar prashantkbio at gmail.com
Tue Jun 28 21:02:59 PDT 2011


Dear Brent,

Use gfortran instead of using g77. Edit config.h file in line FC = g77 to FC
= gfortran. Hope this will solve your problem.

Best regards

Prashant
On Wed, Jun 29, 2011 at 12:30 AM, <dock-fans-request at mailman.docking.org>wrote:

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> Today's Topics:
>
>   1. chimera setup (yp sun)
>   2. Re: chimera setup (Trent E. Balius)
>   3. DOCK 6.4 on Mac OSX? (Brent R. Stockwell)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 28 Jun 2011 19:57:52 +0800 (CST)
> From: yp sun <sunyeping at yahoo.com.cn>
> Subject: [Dock-fans] chimera setup
> To: dock-fans <dock-fans at mailman.docking.org>
> Message-ID:
>        <1309262272.66624.YahooMailClassic at web15608.mail.cnb.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear sir,
> ?
> ???? I want to setup the chimera 1.5.3 program on windows XP system, but
> the setup cannot be finished, it retures a error information that says:
> Unable to excute file: C:/program file/chimera 1.5.3/bin/pythonn.exe.
> ??? How can I solve the problem? Thanks.
>
> Best regards
>
> Yeping Sun PhD
> CAS Key Laboratory of Pathogenic Microbiology & Immunology
> INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
> NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china
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> ------------------------------
>
> Message: 2
> Date: Tue, 28 Jun 2011 08:05:35 -0400
> From: "Trent E. Balius" <tbalius at aol.com>
> Subject: Re: [Dock-fans] chimera setup
> To: sunyeping at yahoo.com.cn, dock-fans at mailman.docking.org
> Message-ID: <8CE03A2D289679A-11EC-1B0A1 at webmail-m009.sysops.aol.com>
> Content-Type: text/plain; charset="us-ascii"
>
>
>  Hi Yeping
>
> Email the chimera mailing list:
>
> chimera-users at cgl.ucsf.edu
>
> Good luck,
>
>
>
> Trent E. Balius
> Graduate Student, Rizzo Group,
> Department of Applied Mathematics and Statistics,
> Stony Brook University.
>
>
> -----Original Message-----
> From: yp sun <sunyeping at yahoo.com.cn>
> To: dock-fans <dock-fans at mailman.docking.org>
> Sent: Tue, Jun 28, 2011 7:57 am
> Subject: [Dock-fans] chimera setup
>
>
>
>
> Dear sir,
>
>     I want to setup the chimera 1.5.3 program on windows XP system, but the
> setup cannot be finished, it retures a error information that says: Unable
> to excute file: C:/program file/chimera 1.5.3/bin/pythonn.exe.
>    How can I solve the problem? Thanks.
>
> Best regards
>
> Yeping Sun PhD
> CAS Key Laboratory of Pathogenic Microbiology & Immunology
> INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
> NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china
>
>
>
> _______________________________________________
> 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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> ------------------------------
>
> Message: 3
> Date: Tue, 28 Jun 2011 12:10:14 -0400
> From: "Brent R. Stockwell" <bstockwell at columbia.edu>
> Subject: [Dock-fans] DOCK 6.4 on Mac OSX?
> To: dock-fans at mailman.docking.org
> Message-ID: <E02F56A1-55E5-4E89-A32E-D6159EDACBEA at columbia.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi folks. I am trying to install DOCK 6.4 on Mac OSX (10.6.8, 2x 3 GHz
> Quad-Core Intel Xeon).
>
> I have not been able to get the install to work. I followed the directions
> in the manual, but when I originally tried the "make all" command, I was
> getting an error related to the lack of g77 compiler. So I was able to
> download and install g77, but I was still getting a bunch of errors abut the
> architecture not being correct:
>
> ld: warning: -macosx_version_min not specificed, assuming 10.6
> ld: warning: ignoring file grid.o, file was built for unsupported file
> format which is not the architecture being linked (i386)
> ld: warning: ignoring file score.o, file was built for unsupported file
> format which is not the architecture being linked (i386)
> etc.
>
> Then, eventually I get this error:
>
> Undefined symbols for architecture i386:
>  "_MAIN__", referenced from:
>      _main in libfrtbegin.a(frtbegin.o)
> ld: symbol(s) not found for architecture i386
> collect2: ld returned 1 exit status
> make[2]: *** [grid] Error 1
> make[1]: *** [utils] Error 2
> make: *** [install] Error 2
>
> I found this discussion on the DOCK-fans archive:
>
> http://mailman.docking.org/pipermail/dock-fans/2011-April/002512.html
>
> and tried modifying the config.h file as suggested, but it did not help. I
> couldn't figure out how to modify the DOCKBUILDFLAGS as suggested there,
> since I didn't see that in the config.h file.
>
> I then found this thread on the DOCK-fans archive:
>
> http://mailman.docking.org/pipermail/dock-fans/2008-August/001699.html
>
> which suggested I should modify the config.h file by editing the LIBS
> definition to:
>
> LIBS=        -lm -lpthread -lSystemStubs
> -L/usr/lib/gcc/powerpc-apple-darwin8/4.0.1 -lgcc
>
> So I did (replacing powerpc-apple-darwin8/4.0.01 with the correct file name
> on my system). But I am still getting this architecture i386 error.
>
> Has anyone successfully installed DOCK 6.4 on Mac OSX 10.6.8, and if so, do
> you have a protocol for how you did it?
>
> Thanks!
>
> Brent
>
>
>
>
>
>
> Brent R. Stockwell, Ph.D.
> Early Career Scientist
> Howard Hughes Medical Institute
> Associate Professor
> Department of Biological Sciences and Department of Chemistry
> Columbia University
> Northwest Corner Building, 12th Floor
> 550 West 120th Street, MC 4846
> New York, NY 10027
> Phone: 212-854-2948
> Fax: 212-854-2951
>
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> End of Dock-fans Digest, Vol 85, Issue 15
> *****************************************
>



-- 
Prashant
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