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PDB format problem...

Hi Modellers!
I have the pdb format problem.
I have the same problem with Stephane Coillet-Matillon's error written at 19 Mar 2002.
Eric Feyfant replied it was a chain identifier problem.
" I corrected Stephane error. It was a chain identifier problem. The chain was specified in the pdb but not in the top file, and Modeler could not extrapolate.
But I don't know how to correct this problem.
How to solve this problem?
The error messages is like this
" Read the alignment from file       : acc_ipn1.ali
Total number of alignment positions:   375
  #  Code        #_Res #_Segm PDB_code    Name
  1       1QJF     331      1        1QJF
  2       ACCO     314      1        ACCO unknown
TOP_________>   121  107 CHECK_ALIGNMENT
check_a_343_> >> BEGINNING OF COMMAND
openf5__224_> Open       11  OLD  SEQUENTIAL  ./1QJF.pdb
rdpdb___303E> No atoms were read from the specified input PDB file:
                1) Possibly because an incorrect/non-existent PDB file is specif
                2) Possibly because the segment is specified incorrectly in the
                   alignment file or by the TOP variable MODEL_SEGMENT. That is,
                   the beginning residue number and/or chain id in MODEL_SEGMENT
                   may not be found in the input PDB file; MODEL_SEGMENT:  1:
              To find out more, switch on maximal output by 'SET OUTPUT_CONTROL
= 1 1 1 1 2'
rdabrk__288W> Protein not accepted:        1
rdabrk__290E> Number of residues in the alignment and  pdb files are different:
     331        0
              For alignment entry:        1
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1
Process System Lab.
Department of Chemical Engineering, Korea University
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