[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: problems with optimaze



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