I am a newbie to Modeller, and am having a problem reading in my template files
in the log I get the error message:
3 lines just before the end bit.....
check_a_343_> >> BEGINNING OF COMMAND
check_a_347E> Structure not read in: 1
recover____E> ERROR_STATUS >=STOP_ON_ERROR: 1 1
All my files (.ali .top .atm .log) are shown below
The 8 template files are in fact all the same (so I just show 1) , just with different filenames, to model different bits of the query sequence.
They are called t2avi1.atm t2avi2.atm ..... t2avi8.atm
I specify which of the 4 chains in the template files to use in the PIR alignment file
in the 4th and 6th fields of the 2nd lines.
My .top script file, .atm template files, and .ali PIR alignment file are all in /home/model/henri/
# Homology modelling by the MODELLER TOP routine 'model'.
INCLUDE # Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log file
SET ALNFILE = 'avi4.ali' # alignment filename
SET ALIGNMENT_FORMAT = 'PIR' #sets alignment format
SET KNOWNS = 't2avi1' 't2avi2' 't2avi3' 't2avi4' 't2avi5' 't2avi6' 't2avi7' 't2avi8' # codes of the templates
SET SEQUENCE = 'avi4' # code of the target
SET ATOM_FILES_DIRECTORY = '/home/model/henri' # directories for input atom files
SET STARTING_MODEL= 1 # index of the first model
SET ENDING_MODEL = 1 # index of the last model
# (determines how many models to calculate)
HEADER BIOTIN BINDING PROTEIN 23-APR-93 2AVI 2AVI 2
REMARK this now a tetramer, created with o, on sunday 22 sept 1996
REMARK by rik wierenga from 2avi.brk
COMPND AVIDIN COMPLEX WITH BIOTIN 2AVI 3
SOURCE HEN EGG-WHITE 2AVI 4
AUTHOR O.LIVNAH,J.SUSSMAN 2AVI 5
REVDAT 1 15-JUL-93 2AVI 0 2AVI 6
REMARK 1 2AVI 7
REMARK 1 REFERENCE 1 2AVI 8
REMARK 1 AUTH O.LIVNAH,E.A.BAYER,M.WILCHEK,J.L.SUSSMAN 2AVI 9
REMARK 1 TITL THREE-DIMENSIONAL STRUCTURES OF AVIDIN AND THE 2AVI 10
REMARK 1 TITL 2 AVIDIN-BIOTIN COMPLEX 2AVI 11
REMARK 1 REF PROC.NAT.ACAD.SCI.USA V. 90 5076 1993 2AVI 12
REMARK 1 REFN ASTM PNASA6 US ISSN 0027-8424 040 2AVI 13
REMARK 2 2AVI 14
REMARK 2 RESOLUTION. 3.0 ANGSTROMS. 2AVI 15
REMARK 3 2AVI 16
REMARK 3 REFINEMENT. 2AVI 17
REMARK 3 PROGRAM XPLOR 2AVI 18
REMARK 3 AUTHORS BRUNGER 2AVI 19
REMARK 3 R VALUE 0.151 2AVI 20
REMARK 3 RMSD BOND DISTANCES 0.013 ANGSTROMS 2AVI 21
REMARK 3 RMSD BOND ANGLE 1.83 DEGREES 2AVI 22
REMARK 4 2AVI 23
REMARK 4 IN EACH MONOMER OF AVIDIN, RESIDUES 1 - 2 AND 124 - 128 2AVI 24
REMARK 4 ARE NOT INCLUDED IN THE ATOM LIST SINCE THE ELECTRON 2AVI 25
REMARK 4 DENSITY IS POOR IN THOSE REGIONS. 2AVI 26
REMARK 5 2AVI 27
REMARK 5 RESIDUE 34 OF EACH CHAIN EXISTS IN TWO FORMS - THR OR ILE. 2AVI 28
REMARK 5 IN THIS ENTRY IT IS PRESENTED AS THR. 2AVI 29
SEQRES 1 A 128 ALA ARG LYS CYS SER LEU THR GLY LYS TRP THR ASN ASP 2AVI 30
SEQRES 2 A 128 LEU GLY SER ASN MET THR ILE GLY ALA VAL ASN SER ARG 2AVI 31
SEQRES 3 A 128 GLY GLU PHE THR GLY THR TYR THR THR ALA VAL THR ALA 2AVI 32
SEQRES 4 A 128 THR SER ASN GLU ILE LYS GLU SER PRO LEU HIS GLY THR 2AVI 33
SEQRES 5 A 128 GLU ASN THR ILE ASN LYS ARG THR GLN PRO THR PHE GLY 2AVI 34
SEQRES 6 A 128 PHE THR VAL ASN TRP LYS PHE SER GLU SER THR THR VAL 2AVI 35
SEQRES 7 A 128 PHE THR GLY GLN CYS PHE ILE ASP ARG ASN GLY LYS GLU 2AVI 36
SEQRES 8 A 128 VAL LEU LYS THR MET TRP LEU LEU ARG SER SER VAL ASN 2AVI 37
SEQRES 9 A 128 ASP ILE GLY ASP ASP TRP LYS ALA THR ARG VAL GLY ILE 2AVI 38
SEQRES 10 A 128 ASN ILE PHE THR ARG LEU ARG THR GLN LYS GLU 2AVI 39
SEQRES 1 B 128 ALA ARG LYS CYS SER LEU THR GLY LYS TRP THR ASN ASP 2AVI 40
SEQRES 2 B 128 LEU GLY SER ASN MET THR ILE GLY ALA VAL ASN SER ARG 2AVI 41
SEQRES 3 B 128 GLY GLU PHE THR GLY THR TYR THR THR ALA VAL THR ALA 2AVI 42
SEQRES 4 B 128 THR SER ASN GLU ILE LYS GLU SER PRO LEU HIS GLY THR 2AVI 43
SEQRES 5 B 128 GLU ASN THR ILE ASN LYS ARG THR GLN PRO THR PHE GLY 2AVI 44
SEQRES 6 B 128 PHE THR VAL ASN TRP LYS PHE SER GLU SER THR THR VAL 2AVI 45
SEQRES 7 B 128 PHE THR GLY GLN CYS PHE ILE ASP ARG ASN GLY LYS GLU 2AVI 46
SEQRES 8 B 128 VAL LEU LYS THR MET TRP LEU LEU ARG SER SER VAL ASN 2AVI 47
SEQRES 9 B 128 ASP ILE GLY ASP ASP TRP LYS ALA THR ARG VAL GLY ILE 2AVI 48
SEQRES 10 B 128 ASN ILE PHE THR ARG LEU ARG THR GLN LYS GLU 2AVI 49
HET BTN A 150 16 BIOTIN 2AVI 50
HET NAG A 340 14 N-ACETYL-D-GLUCOSAMINE 2AVI 51
HET BTN B 150 16 BIOTIN 2AVI 52
HET NAG B 341 14 N-ACETYL-D-GLUCOSAMINE 2AVI 53
FORMUL 3 BTN 2(C10 H16 N2 O3 S1) 2AVI 54
FORMUL 4 NAG 2(C8 H15 N1 O5) 2AVI 55
FORMUL 5 HOH *74(H2 O1) 2AVI 56
CRYST1 72.150 80.370 43.540 90.00 90.00 90.00 C 21 21 2 8 2AVI 57
ORIGX1 1.000000 0.000000 0.000000 0.00000 2AVI 58
ORIGX2 0.000000 1.000000 0.000000 0.00000 2AVI 59
ORIGX3 0.000000 0.000000 1.000000 0.00000 2AVI 60
SCALE1 0.013860 0.000000 0.000000 0.00000 2AVI 61
SCALE2 0.000000 0.012442 0.000000 0.00000 2AVI 62
SCALE3 0.000000 0.000000 0.022967 0.00000 2AVI 63
ATOM 1 N LYS A 3 -2.040 13.882 -0.329 1.00 28.24 2AVI 64
ATOM 2 CA LYS A 3 -2.951 14.933 0.253 1.00 28.81 2AVI 65
ATOM 3 C LYS A 3 -2.548 15.170 1.710 1.00 26.30 2AVI 66
ATOM 4 O LYS A 3 -2.067 14.247 2.374 1.00 26.95 2AVI 67
ATO,,,,,,
and so on
MODELLER 6v2, 17 Feb 2002
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2002 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from A. Fiser, R. Sanchez, M.A. Marti-Renom,
B. Jerkovic, A. Badretdinov, F. Melo,
J.P. Overington & E. Feyfant
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 modeling.bio.jyu.fi 2.4.18-14 i686
Date and time of compilation : 07/05/2002 17:08:33
Job starting time (YY/MM/DD HH:MM:SS): 2002/11/08 20:34:11.701
TOP_________> 105 705 SET ALNFILE = 'avi4.ali'
TOP_________> 106 706 SET ALIGNMENT_FORMAT = 'PIR'
check_a_343_> >> BEGINNING OF COMMAND
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]: 18672759 18235.120 17.808
Starting time : 2002/11/08 20:34:11.701
Closing time : 2002/11/08 20:34:15.869
Total CPU time [seconds] : 2.25
http://www.chalkie.org.uk
Daniel James White PhD.
Cell Biology
Department of Biological and Environmental Science
University of Jyväskylä
FIN-40351
Jyväskylä
Finland