(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.