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: reche@research.dfci.harvard.edu 44 Binney Street, D1510A, EM: reche@mifoundation.org Boston, MA 02115 URL: http://www.reche.org *******************************************************************