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 = '$(JOB).rsr', RESULT = LOOP_CSRFILE assgn___E> cannot assign a value to a value: ------------------------------------------------------------------------------- Do you know what went wrong? Thanks. Tom
Tom Lee wrote: > > Hi, > > I have generated a model for my molecule. I'm trying to study a loop > region in detail. I followed the instruction in FAQ of the manual and > wrote the following Top file: > > ------------------------------------------------------------------------------- > INCLUDE > SET SEQUENCE = 'ASLA2' > SET MODEL = 'ASLA2.B99990001.pdb' > SET ATOM_FILES_DIRECTORY = './:../atom_files' > SET OUTPUT_DIRECTORY = './' > SET PDB_EXT = '.pdb' > SET STARTING_MODEL = 20 > SET ENDING_MODEL = 29 > SET MD_LEVEL = 'refine1' > SET RAND_SEED = -34871 > CALL ROUTINE = 'loop' > > CALL ROUTINE = 'cluster', ID1 = 20, ID2 = 29 > > SUBROUTINE ROUTINE = 'select_atoms' > > PICK_ATOMS SELECTION_SEGMENT = '49:' '76:', SELECTION_STATUS = 'initialize' > > RETURN > END_SUBROUTINE > > ----------------------------------------------------------------------------- > > "ASLA2.B99990001.pdb" is the file generated by the previous Modeler run. > "49" and "76" are the starting and ending residues of the loop region. > I got an error message after running this job: > > ------------------------------------------------------------------------------- > TOP______> 102 414 STRING_OPERATE OPERATION = 'CONCATENATE', ; > STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; > LE > > TOP______> 103 415 SET ROOT_NAME = SEQUENCE > > TOP______> 104 416 RETURN > > TOP______> 105 591 STRING_OPERATE OPERATION = 'CONCATENATE', ; > STRING_ARGUMENTS = '$(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
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
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Andras Fiser -
Tom Lee