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.