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[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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