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
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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*
Joel Tyndall
Modeller Caretaker