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: ursula@salilab.org phone: 415-514-4233

On 7/17/03 8:33, "Rolando Pajon Feyt" rolando.pajon@cigb.edu.cu 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:modeller-care@salilab.org] > Sent: Thursday, July 17, 2003 10:03 AM > To: modeller_usage@salilab.org > Cc: Feng Cui > Subject: FW: help > > > > > Message forwarded by list owner > > ------ Forwarded Message > From: Feng Cui fengcui@iastate.edu > Date: Wed, 16 Jul 2003 18:05:51 -0500 (CDT) > To: modeller-care@salilab.org > 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 > > > >