[modeller_usage] Metal ions

[Joel Tyndall <>]

Hi message board,

I have been trying to include a zinc atom in my model based on the same 
ion in the template but I just can't crack it. I have attached all 
relevant files and log file. I am using mod8v2.

Advice is much appreciated

Cheers

Joel

--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand                     

Pukenga
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Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
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Attachment: 2fk4.pdb
Description: application/save-as

                         MODELLER 8v2, Feb 28, 2006 05:48pm

     PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS

                                                                   
                     Copyright(c) 1989-2006 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, M. Topf, 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, Linux allroy.otago.ac.nz 2.6.9-5.ELsmp x86_64
Date and time of compilation         : 02/28/2006 18:38:42
MODELLER executable type             : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2006/07/07  09:55:15.134

rdabrk__290E> Number of residues in the alignment and  pdb files are different:       66       65
              For alignment entry:        1  2fk4
                                 x  (mismatch at alignment position     66)
 Alignment   FHNIRGRWTGRCMSCSRSSRz                                        
       PDB   FHNIRGRWTGRCMSCSRSSR                                         
     Match   ********************                                         

  Please check your alignment file header to be sure you correctly specified
  the starting and ending residue numbers and chains. The alignment sequence
  must match that from the atom file exactly.

  Another possibility is that some residues in the atom file are missing,
  perhaps because they could not be resolved experimentally. (Note that Modeller
  reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
  In this case, simply replace the section of your alignment corresponding
  to these missing residues with gaps.
check_a_337E> Structure not read in (please consult the log file
              for more details):        1  2fk4
top_error__E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

Dynamically allocated memory at          finish [B,kB,MB]:      2331663    2277.015     2.224
Starting time                                            : 2006/07/07  09:55:15.134
Closing time                                             : 2006/07/07  09:55:16.008
Total CPU time [seconds]                                 :       0.87

INCLUDE
SET ALNFILE = 'hpv_16_e6_Nterm_2fk4.ali'
SET KNOWNS = '2fk4'
SET SEQUENCE = 'hpv_16_Nterm_e6'
SET STARTING_MODEL = 1
SET ENDING_MODEL = 5
CALL ROUTINE = 'model'
SET HETATM_IO = on

>P1;2fk4
structureX:2fk4:   3 :A: 68 :::::
SYSLYGTTLEQQYNKPLSDLLIRCINCQKPLSPEEKQRHLDKKQRFHNIRGRWTGRCMSCSRSSR/z*


>P1;hpv_16_Nterm_e6
sequence:hpv_16_Nterm_e6:     : :    : ::: 0.00: 0.00
PRKLP--QLCTELQTTIHDIILECVYCKQQLLRREVYDFAFRDLCIVYRDGNPYAVCDKCLKFYS/z*