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Re: help running run_tops1



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
> 
> 
> 
>