[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[modeller_usage] modeller error



Dear sir
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


Celebrate Yahoo!'s 10th Birthday!
Yahoo! Netrospective: 100 Moments of the Web