i have just started using modeller7v7 but have landed in to some problems.i have a few doubts

1. which directory should i place the top files, ali files and the pdb files. i placed top files in the bin, pdb files in atom-files directory. and tried to run the command, but it shows this error

MODELLER 7v7, Sep 12, 2004 09:15pm

PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS

                     Copyright(c) 1989-2004 Andrej Sali
                            All Rights Reserved

                             Written by A. Sali
                               with help from
           B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom,
                     N. Eswar, F. Alber, B. Oliva, A. Fiser,
                    R. Sanchez, B. Yerkovich, A. Badretdinov,
                      F. Melo, J.P. Overington, E. Feyfant
                 University of California, San Francisco, USA
                    Rockefeller University, New York, USA
                      Harvard University, Cambridge, USA
                   Imperial Cancer Research Fund, London, UK
              Birkbeck College, University of London, London, UK

Kind, OS, HostName, Kernel, Processor: 4, Win2000 build 2195 Service Pack 4, PROJECTBT, uni, x86 Family 15 Model 2 Stepping 9
Date and time of compilation : 09/13/2004 17:17:22
Job starting time (YY/MM/DD HH:MM:SS): 2004/12/27 13:26:51.093

TOP_________>   109 749 SET ALNFILE = 'seqalin.ali'

TOP_________>   110 750 SET KNOWNS   = '1ocs'

TOP_________>   111 751 SET SEQUENCE = 'yhr'

TOP_________>   112 752 SET ATOM_FILES_DIRECTORY = './:../atom_files'

TOP_________>   113 753 SET STARTING_MODEL = 1

TOP_________>   114 754 SET ENDING_MODEL = 1

TOP_________>   115 755 CALL ROUTINE = 'model'

TOP_________>   116 419 CALL ROUTINE = 'getnames'

TOP_________>   117 534 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION;
                       = 'EQ', THEN =     'STRING_OPERATE OPERATION = CONCATENA;
                      TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL'

TOP_________>   118 535 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI;
                      ON = 'EQ', THEN =     'STRING_OPERATE OPERATION = CONCATE;
                      NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE;
                      '

TOP_________>   119 536 STRING_OPERATE OPERATION = 'CONCATENATE',                ;
                         STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE

TOP_________>   120 537 STRING_OPERATE OPERATION = 'CONCATENATE',                ;
                        STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI;
                      LE

TOP_________>   121 538 SET ROOT_NAME = SEQUENCE

TOP_________>   122 539 RETURN

TOP_________>   123 420 CALL ROUTINE = 'homcsr'

TOP_________>   124 112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE;
                      NCE

Dynamically allocated memory at         amaxseq [B,kB,MB]:        84067      82.097     0.080
fullfn__230E> File not found: seqalin.ali
              Directories:
              Extensions : :.ali
              Prefixes   : nothing, pdb
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

Dynamically allocated memory at          finish [B,kB,MB]:        84067      82.097     0.080
Starting time                                            : 2004/12/27 13:26:51.093
Closing time                                             : 2004/12/27 13:26:52.078
Total CPU time [seconds]                                 :       0.97