[modeller_usage] clustering problem

Dear Modeller, I try to do a loop modeling using the following script. I got the xxx.BL####0000.pdb and DL#### output files, but the job stop at the step for clustering, the error showed like that:

TOP_________> 1512 686 END_DO

TOP_________> 1513 687 RETURN

TOP_________> 1514 748 CALL ROUTINE = 'cluster', ID1 = 1, ID2 = 20

TOP_________> 1515 606 IF ARGUMENTS CLUSTER_CUT 0, OPERATION = 'LT', THEN = 'SET; CLUSTER_CUT = 1.5'

TOP_________> 1516 607 READ_MODEL FILE = MODEL, ALIGN_CODES = ROOT_NAME

pdbnam__217W> Filename for PDB code not found: undefined Directories: ./:../atom_files Extensions : :.atm:.pdb:.ent:.crd openf5__224_> Open 11 OLD SEQUENTIAL file-not-found openf5__225E> File does not exist: file-not-found openf5__224_> Open 11 OLD SEQUENTIAL file-not-found openf5__225E> File does not exist: file-not-found rdatm___297_> Segments, residues, atoms: 1 319 2467 rdatm___298_> Segment: 1 C 2467 iatmcls_286W> MODEL atom not classified: UNK: UNK iatmcls_286W> MODEL atom not classified: UNK: UNK iatmcls_286W> MODEL atom not classified: UNK: UNK iatmcls_286W> MODEL atom not classified: UNK: UNK iatmcls_286W> MODEL atom not classified: UNK: UNK ................... Dynamically allocated memory at amaxseq [B,kB,MB]: 22095569 21577.703 21.072 pdbnam__217W> Filename for PDB code not found: YpkA.BL99990001.pdb Directories: ./:../atom_files Extensions : :.atm:.pdb:.ent:.crd rdabrk__288W> Protein not accepted: 1 pdbnam__217W> Filename for PDB code not found: YpkA.BL99990002.pdb Directories: ./:../atom_files Extensions : :.atm:.pdb:.ent:.crd ............... fndatmi_285W> Number of residues <> number of atoms; atom code: 319 168 CA fndatmi_284E> Beginning atom index for a residue out of bounds: 0 0 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1

Could you please help me figure out the problem?

Thank you very much!

Xin

Here is the top file:

=============== INCLUDE #DEFINE_STRING VARIABLES = LOOP_CSRFILE LOOP_INI_MODEL SET OUTPUT_CONTROL = 1 1 1 1 1 SET SEQUENCE = 'YpkA' SET LOOP_MODEL = 'YpkA_modelB.pdb' SET ATOM_FILES_DIRECTORY = './:../atom_files' SET PDB_EXT = '.pdb' SET LOOP_STARTING_MODEL = 1 SET LOOP_ENDING_MODEL = 20 SET LOOP_MD_LEVEL = 'refine_3' SET RAND_SEED = -21840

CALL ROUTINE = 'loop'

CALL ROUTINE = 'cluster', ID1 = 1, ID2 = 20

SUBROUTINE ROUTINE = 'select_loop_atoms' PICK_ATOMS SELECTION_SEGMENT = '203:' '256:', SELECTION_STATUS = 'initialize' RETURN END_SUBROUTINE ==============

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