(note: I have installed modeller6v2 in Linux Suse 8.1. When execute modeller with the examples , modeller execute correctly . If the files "model-default.top" and "alignment.ali" in the directory "tutorial-model" are copy in other directory and execute the process (mod6v2 model-default.top) run correctly obtain the new model for target sequence )
hi
I have a problem to run modeller
I create my alignment file (alignment.ali) and top file (model-default.top) ,but to run "mod6v2 model-default.top" the log file to show the not execute the process. and the log file no show errors.
which can be the problem?
the files are:
alignment.ali
C; A sample alignment in the PIR format; used in tutorial >P1;1f36A structureX:1f36:10 :A :98 :A : : : : VLTVSTVNSQDQVTQKPLRDSVKQALENYFAQLNGQDVNDLYELVLAEVEQPLLDMVMQYTRGNQTRAALMMGINRGTLRKKLKKYGMN* >P1;sec1 sequence:sec1:1 :A :89 :A : : : : VLTVSTVNSQAQVTQKPLRDSVKQALKNYFAQLNGQDVSDLYELVLAEVEQPLLDMVMQYTRGNQTRAALMMGINRGTLRKKLKKYGMN*
model-default.top
# Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'alignment.ali' # alignment filename SET KNOWNS = '1f36A' # codes of the templates SET SEQUENCE = 'sec1' # code of the target SET ATOM_FILES_DIRECTORY = '/data1' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling
model-default.log
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, Linux bioinf4 2.4.19-4GB i686 Date and time of compilation : 07/16/2002 11:42:16 Job starting time (YY/MM/DD HH:MM:SS): 2003/04/17 14:05:48.759 TOP_________> 105 705 SET ALNFILE = 'alignment.ali'
TOP_________> 106 706 SET KNOWNS = '1f36A'
TOP_________> 107 707 SET SEQUENCE = 'sec1'
TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = '/data1'
TOP_________> 109 709 SET STARTING_MODEL = 1
TOP_________> 110 710 SET ENDING_MODEL = 1
Dynamically allocated memory at finish [B,kB,MB]: 2200483 2148.909 2.099 Starting time : 2003/04/17 14:05:48.759 Closing time : 2003/04/17 14:05:51.710 Total CPU time [seconds] : 2.87
the log file no show errors and show that the process is not execute.
which can be the problem? I need Help
The modeller have other file where save logs?
thanks...