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:fisera@rockvax.rockefeller.edu > 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