[modeller_usage] prb encountered, plz help

[rathankar rao <>]

i had to model a protein whose ali file, top file and the log files are present here. i couldnt model it and its always presenting some or the other errors plz help

 

there was one problem in the pdb file,:

a ligand cme under the name of the heteroatom, had a residue number as 91 , which was supposed to be a number for the aminoacid. the next residue thus continued from 92 and so on. so i changed the residue numbers by 1. i changed the ligand atom number also as 1191 instead of 91 so that it is distinguished from the other aminoacids. despite all these it dosent work.

i have one more doubt , if at all the protein as many chains then how do i model it. what is the command which is used to model a protein with chains. plz explain

with regadrs

rathankar

 

 

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>P1;1ocs
structureX:1ocs:30:A:160:A:yhr: yeast:2.03:0.217
AEPENFLEIEVHNPKTHIPNGMDSKGMFTDYEIICRTNLP------SFHKRVSKVRRRYSDFEFFRKLIKEISML
NHPKV----MVPHLPGKILLSN-------RFSNEVIEERRQGLNTWMQSVAGHPLLQSGSKVLVR-FIEAEKFV*

>P1;yhr
sequence:yhr:1: :149: :yhr: yeast: 2.00: -1.00
SINANFSFQKAHVSDCTIVNG-DHGTKFAVWRITVFLEPNLKAFAAKRESYKIQTYKRYSDFVRLRENLLTRIKT
AKPEKLNCLQIPHLPPSVQWYSSWKYQEVNLNKDWLAKRQRGLEYFLNHIILNSSLVEMTKDILIQFLEPSKRV*


# Fichier d'entree pour la procedure 'model'

INCLUDE

SET OUTPUT_CONTROL = 1 1 1 1 1

SET ALNFILE  = 'yhr.ali'

SET KNOWNS  = '1ocs' #

SET SEQUENCE  = 'yhr' #

SET ATOM_FILES_DIRECTORY = './:../atom_files'

SET STARTING_MODEL= 1

SET ENDING_MODEL= 1 

CALL ROUTINE = 'model'


                         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, WinME build  4114, TJAY-4, uni, x86 Family   6 Model  3 Stepping  0
Date and time of compilation         : 09/13/2004 17:17:22
Job starting time (YY/MM/DD HH:MM:SS): 2004/04/25  20:21:56.690

TOP_________>   109  749 SET ALNFILE  = 'yhr.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
openf5__224_> Open       20  OLD  SEQUENTIAL  yhr.ali

Dynamically allocated memory at         amaxbnd [B,kB,MB]:      2743707    2679.401     2.617
openf5__224_> Open       20  OLD  SEQUENTIAL  yhr.ali

Read the alignment from file       : yhr.ali
Total number of alignment positions:   149

  #  Code        #_Res #_Segm PDB_code    Name
-------------------------------------------------------------------------------
  1       1ocs     131      1        1ocs yhr
  2        yhr     148      1         yhr yhr
TOP_________>   125  113 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER;
                      ATION = 'ne', THEN = 'GO_TO __ACCELRYS1' 
 
TOP_________>   126  117 CHECK_ALIGNMENT 
 
check_a_343_> >> BEGINNING OF COMMAND
pdbnam__217W> Filename for PDB code not found:  1ocs
              Directories:  ./:../atom_files
              Extensions :   :.atm:.pdb:.ent:.crd
rdabrk__288W> Protein not accepted:        1
check_a_337E> Structure not read in:        1
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

Dynamically allocated memory at          finish [B,kB,MB]:      2743857    2679.548     2.617
Starting time                                            : 2004/04/25  20:21:56.690
Closing time                                             : 2004/04/25  20:22:01.300
Total CPU time [seconds]                                 :       4.61