Try commenting out: #Example for: OPTIMIZE, SWITCH_TRACE

MODELLER is reading it as a command, which of course doesn't exist... ;-)

Best, Bozidar

On Tue, 13 Aug 2002, Pedro A Reche wrote:

> 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 > ******************************************************************* > >