Tom Lee wrote:
>
> Hi,
>
> I have generated a model for my molecule. I'm trying to study a loop
> region in detail. I followed the instruction in FAQ of the manual and
> wrote the following Top file:
>
> -------------------------------------------------------------------------------
> INCLUDE
> SET SEQUENCE = 'ASLA2'
> SET MODEL = 'ASLA2.B99990001.pdb'
> SET ATOM_FILES_DIRECTORY = './:../atom_files'
> SET OUTPUT_DIRECTORY = './'
> SET PDB_EXT = '.pdb'
> SET STARTING_MODEL = 20
> SET ENDING_MODEL = 29
> SET MD_LEVEL = 'refine1'
> SET RAND_SEED = -34871
> CALL ROUTINE = 'loop'
>
> CALL ROUTINE = 'cluster', ID1 = 20, ID2 = 29
>
> SUBROUTINE ROUTINE = 'select_atoms'
>
> PICK_ATOMS SELECTION_SEGMENT = '49:' '76:', SELECTION_STATUS = 'initialize'
>
> RETURN
> END_SUBROUTINE
>
> -----------------------------------------------------------------------------
>
> "ASLA2.B99990001.pdb" is the file generated by the previous Modeler run.
> "49" and "76" are the starting and ending residues of the loop region.
> I got an error message after running this job:
>
> -------------------------------------------------------------------------------
> TOP______> 102 414 STRING_OPERATE OPERATION = 'CONCATENATE', ;
> STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI;
> LE
>
> TOP______> 103 415 SET ROOT_NAME = SEQUENCE
>
> TOP______> 104 416 RETURN
>
> TOP______> 105 591 STRING_OPERATE OPERATION = 'CONCATENATE', ;
> STRING_ARGUMENTS = '$(JOB).rsr', RESULT = LOOP_CSRFILE
>
> assgn___E> cannot assign a value to a value:
>
> -------------------------------------------------------------------------------
>
> Do you know what went wrong?
>
> Thanks.
>
> Tom
The routine looks good, works for me with an other example than it was written
in the manual. Check your file names and extension used by the program to be
sure that the program reads the correct files.
include in your top file:
SET OUTPUT_CONTROL = 1 1 1 1
this will write out everything to your log file,line by line, so you should
see what goes wrong.
Andras
--
,
Andras Fiser, PhD # phone: (212) 327 7206
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras