On Mon, 27 Jul 1998, Andras Fiser wrote:
> 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 = '$(JOB).rsr', RESULT = LOOP_CSRFILE
> >
> > assgn___E> cannot assign a value to a value:
> >
> > -------------------------------------------------------------------------------
> >
> > Do you know what went wrong?
> >
> > Thanks.
> >
> > Tom
>
>
> The routine looks good, works for me with an other example than it was written
> in the manual. Check your file names and extension used by the program to be
> sure that the program reads the correct files.
>
> include in your top file:
>
> SET OUTPUT_CONTROL = 1 1 1 1
>
> this will write out everything to your log file,line by line, so you should
> see what goes wrong.
>
>
> Andras
>
>
> --
> ,
> Andras Fiser, PhD # phone: (212) 327 7206
> The Rockefeller University # fax: (212) 327 7540
> Box 270, 1230 York Avenue # e-mail:
> New York, NY 10021-6399, USA # http://salilab.org/~andras
>
Thank you for the help. I checked the filename and it was correct.
ASLA2.B99990001.pdb is the coordinate file generated by Modeler and it is
in the working directory. I included the SET OUTPUT_CONTROL = 1 1 1 1,
which made the TOP file look like this:
=
INCLUDE
SET SEQUENCE = 'ASLA2'
SET MODEL = 'ASLA2.B99990001.pdb'
SET ATOM_FILES_DIRECTORY = './:../atom_files'
SET OUTPUT_DIRECTORY = './'
SET OUTPUT_CONTROL = 1 1 1 1
SET PDB_EXT = '.pdb'
SET STARTING_MODEL = 20
SET ENDING_MODEL = 29
SET MD_LEVEL = 'refine1'
SET RAND_SEED = -34871
CALL ROUTINE = 'loop'
CALL ROUTINE = 'cluster', ID1 = 20, ID2 = 29
SUBROUTINE ROUTINE = 'select_atoms'
PICK_ATOMS SELECTION_SEGMENT = '49:' '76:', SELECTION_STATUS = 'initialize'
RETURN
END_SUBROUTINE
However, the job was terminated the same way as before. The .log file
looks just the same, and doesn't tell me anything more:
........
TOP______> 104 415 SET ROOT_NAME = SEQUENCE
TOP______> 105 416 RETURN
TOP______> 106 591 STRING_OPERATE OPERATION = 'CONCATENATE', ;
STRING_ARGUMENTS = '$(JOB).rsr', RESULT = LOOP_CSRFILE
assgn___E> cannot assign a value to a value:
What does the last line mean? I'm using the Modeler purchased from MSI.
We bought it a couple months ago. Is it the same version as the one on
the Rockefeller web site? Does it make any difference? Thanks.
Tom