Hi all,
I am trying to optimaze a model by just running the follwing script:
Example for: OPTIMIZE, SWITCH_TRACE
# This will optimize stereochemistry of a given model, including
# non-bonded contacts.
READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib'
READ_PARAMETERS FILE = '$(LIB)/par.lib'
READ_MODEL FILE = '1c11'
SEQUENCE_TO_ALI ATOM_FILES = '1c11', ALIGN_CODES = '1c11'
SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES
'1c11.ini', ;
ALIGN_CODES = ALIGN_CODES '1c11-ini'
GENERATE_TOPOLOGY SEQUENCE = '1c11-ini'
TRANSFER_XYZ
BUILD_MODEL INITIALIZE_XYZ = off
WRITE_MODEL FILE = '1c11.ini'
# Generate the restraints:
MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo'
WRITE_RESTRAINTS FILE = '1c11.rsr'
ENERGY DYNAMIC_SPHERE = on
SWITCH_TRACE TRACE_OUTPUT = 1, FILE = '1c11.trc'
OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 20
OPTIMIZE OPTIMIZATION_METHOD = 3, TEMPERATURE = 300, MAX_ITERATIONS
= 50
OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 20
ENERGY
WRITE_MODEL FILE = '1c11.B'
Unfortunally, I am getting the an error after running mod optimaze.top,
and I do not see what is wrong, possble something silly but I do not
wee where the problem is. So any help will be very welcomed. 1c11 is the
name of the model. I moved
Here it follows the optimaze.log
1c11.B99990001 to 1c11.
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 mif.dfci.harvard.edu
2.4.13 i686
Date and time of compilation : 05/24/2002 09:27:23
Job starting time (YY/MM/DD HH:MM:SS): 2002/08/13 12:19:52.681
rdactio_534E> Command not recognized: EXAMPLE FOR: OPTIMIZE,
SWITCH_TRACE
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]:
2190959 2139.608 2.089
Starting time : 2002/08/13
12:19:52.681
Closing time : 2002/08/13
12:19:54.367
Total CPU time [seconds] : 1.58
--
*******************************************************************
PEDRO A. RECHE , pHD TL: 617 632 3824
Dana-Farber Cancer Institute, FX: 617 632 4569
Harvard Medical School, EM:
44 Binney Street, D1510A, EM:
Boston, MA 02115 URL:
http://www.reche.org
*******************************************************************