It was a little early this morning when I forwarded Feng's message, I should
have answered it right then.
The run_tops1 file is not a modeller top file. It is a script that runs a
number of modeller jobs. This is the content:
run_tops1:
#!/bin/sh
mod6v2 initial
mod6v2 model-default
mod6v2 model-segment
mod6v2 model-fast
mod6v2 model-loop
# procheck 1fdx.B999901 2.0
mod6v2 compare
It is a unix shell script.
In a unix environment, you would execute it like this:
cd whereever/examples/tutorial-model
./run_tops1
all those top files (initial.top, model-default.top, etc.) are in this
directory.
For windows, you should remove the first line of the script and the procheck
line (commented out in the unix script), and rename it run_tops1.bat. Then
you should change mod6v2 to mod, execute the modenv.bat file to set the
environment, and execute it as run_tops1 from the tutorial-model directory.
Hope this solves your problem.
Best regards,
Ursula
----------------------------------------------
Ursula Pieper, Ph.D.
Laboratory of Andrej Sali
Mission Bay Genentech Hall
600 16th Street, Suite N474P
University of California, San Francisco
San Francisco, CA 94143-2240
email: phone: 415-514-4233
On 7/17/03 8:33, "Rolando Pajon Feyt" <> wrote:
> Dear all:
>
> I have de very same problem (see message below). Can anyone help us?
>
> Regards
>
> rolando
>
> Dr. Rolando Pajón Feyt
>
> Head of Meningococcal Reseach Department
>
> Vaccine Division
>
> Centro de Ingeniería Genética y Biotecnología
>
> Ave 31 e/ 158 y 190, Cubanacán, Playa.
>
> PO BOX 6162
>
> Ciudad Habana
>
> CP 10600
>
> Cuba
>
> Volverán
>
>
>
>
> -----Original Message-----
> From: Modeller Care [">mailto:]
> Sent: Thursday, July 17, 2003 10:03 AM
> To:
> Cc: Feng Cui
> Subject: FW: help
>
>
>
>
> Message forwarded by list owner
>
> ------ Forwarded Message
> From: Feng Cui <>
> Date: Wed, 16 Jul 2003 18:05:51 -0500 (CDT)
> To:
> Subject: help
>
>
> Sir,
>
> i downloaded the Modeller 6v2 on my laptop (windows xp). i modified the
> mod.bat and modenv.bat based on the Readme file. i tried to run a test case
> upon the window command prompt. but the program seems not to be ale to
> recognize the MOD6V2 command. the error message is following:
>
> C:\Downloads\modeller6v2\bin>mod.bat ..\examples\tutorial-model\run_tops1
>
> C:\Downloads\modeller6v2\bin>set MODINSTALL6v2=c:\Downloads\modeller6v2
>
> C:\Downloads\modeller6v2\bin>set KEY_MODELLER6v2=XXX
>
> C:\Downloads\modeller6v2\bin>set LIBS_LIB6v2=c:\Downloads\modeller6v2
> \modlib\lib
> s.lib
>
> C:\Downloads\modeller6v2\bin>set EXECUTABLE_TYPE6v2=i386-windf
>
> C:\Downloads\modeller6v2\bin>set PATH=c:\Downloads\modeller6v2
> \bin;C:\Perl\bin\;
> C:\texmf\miktex\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32
> \Wbem;C:\P
> rogram Files\Common Files\Adaptec Shared\System;c:\matlab6p5
> \bin\win32;C:\KERB;C
> :\j2sdk1.4.1_02\bin;c:\Downloads\modeller6v2\bin;c:\Downloads\modeller6v2
> \bin;c:
> \Downloads\modeller6v2\bin;c:\Downloads\modeller6v2
> \bin;c:\Downloads\modeller6v2
> \bin;c:\Downloads\modeller6v2\bin
>
> C:\Downloads\modeller6v2\bin>c:\Downloads\modeller6v2
> \bin\modeller6v2 ..\example
> s\tutorial-model\run_tops1
>
> MODELLER 6v2, 17 Feb 2002
>
> PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
>
>
> Copyright(c) 1989-2002 Andrej Sali
> All Rights Reserved
>
> Written by A. Sali
> with help from A. Fiser, R. Sanchez, M.A. Marti-Renom,
> B. Jerkovic, A. Badretdinov, F. Melo,
> J.P. Overington & E. Feyfant
> Rockefeller University, New York, USA
> Harvard University, Cambridge, USA
> Imperial Cancer Research Fund, London, UK
> Birkbeck College, University of London, London, UK
>
>
> Kind, OS, HostName, Kernel, Processor: 4, Windows_NT WUGRADS x86 Family 15
> Model
> 2 Stepping 7, Genuine
> Date and time of compilation : Jul 09 2002 16:21:30
> Job starting time (YY/MM/DD HH:MM:SS): 2003/07/16 17:53:12.039
>
> rdactio_534E> Command not recognized: MOD6V2 INITIAL
> recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
>
> Dynamically allocated memory at finish [B,kB,MB]: 2190959
> 2139.
> 608 2.089
> Starting time : 2003/07/16
> 17:53:12.
> 039
> Closing time : 2003/07/16
> 17:53:13.
> 200
> Total CPU time [seconds] : 0.91
>
> C:\Downloads\modeller6v2\bin>
>
> please let me know what i should do. thanks.
>
> Feng Cui
>
>
>
>
>
>
>
> ------ End of Forwarded Message
>
>
>
>