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:
> 44 Binney Street, D1510A, EM:
> Boston, MA 02115 URL:
> http://www.reche.org
> *******************************************************************
>
>