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Tutorial from CPIB



Hello again,
   Jim, I tried your suggestion of using fewer
randomizations to run Modeller but apparently, that
was not the problem.  I'm now certain that my
computer can not handle a full run of Modeller. 
I've switched over to running the program from a
server and that made the first part of the tutorial
work.  Looking at the example in the manual - as I
interpret it - the writer suggests that using 20
randomizations would be good for a trial run but
real work would require it to be set to 100.
   Now I am faced with another problem.  I have gone
through the example in the first tutorial from 

http://salilab.org/modeller/user_manual.shtml

and am unable to run the model-single.top script.  I
am wondering why it will not recognize the files in
my directory to generate models.  It delivers the
following error.  

                         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, IRIX64 EBI
6.5 IP30
Date and time of compilation         : 07/05/2002
17:12:26
Job starting time (YY/MM/DD HH:MM:SS): 2003/08/05 
22:15:20.967

rdabrk__291E> Sequence difference between alignment
and  pdb :

   STRUCTURE RES_IND  ALN_ITYP  ALN_RES  X_ITYP 
X_RES  -----*-----
           1       1         6     GLY       35  
ACE   -----GSEPIR
check_a_337E> Structure not read in:        1
recover____E> ERROR_STATUS >= STOP_ON_ERROR:       
1       1

Dynamically allocated memory at          finish
[B,kB,MB]:      7075381    6909.552     6.748
Starting
time                                            :
2003/08/05  22:15:20.967
Closing
time                                             :
2003/08/05  22:15:24.899
Total CPU time
[seconds]                                 :       0.00


   Any thoughts as to why the message reads
check_a_337 would be appreciated.  I am not sure as
to why the file is not being found.  


Thanks.

Andrew Latos
MMBB
University of Idaho

PS
Antonio Luque: you are running the program without a
script file or .top file to tell it what to do. 
Look up the link above for sample files to work
with.  The line you type in may look like 

>c:\modeller6v2\bin\modeller6v2 compare.top

I may be wrong about that since I'm not using
windows to run the program.