Running Modeller6v2 Windows

7 Apr 2003


      Hi,
    I am new to Modeller. I am having problems running the modeller
windows version on XP. I am trying to run the following top file using the
command:
mod model-default.top
INCLUDE
READ_ALIGNMENT DIRECTORY = 'C:\mod6v2\alignments', FILE =
'1L9H_O2D2.ali', ALIGNMENT_FORMAT = 'PIR'
SET KNOWNS     = '1l9h'
SET SEQUENCE   = 'O2D2'
SET ATOM_FILES_DIRECTORY = 'C:\mod6v2\pdb', ATOM_FILES = '1l9h.atm'
SET OUTPUT_CONTROL = 1 1 1 1 1
SET STARTING_MODEL = 1
SET ENDING_MODEL = 3
CALL ROUTINE    = 'model'
The alignment file is itself
>1l9h
>structure:1l9h:1    :A:349:A:Bacterorhodopsin:Archae Bacteria:1.5:-1
---MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKK
LRT------PLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVF---------GPTGCNLEGFFATLGGE
IALWSLVVLAIERYVVVCKPMSNFRFG----------ENHAIMGVAFTWVMALACAAPPLVGWSRYIPEG
MQCSCGIDYYTPHEETN--------NESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAA-----ATT-
-QKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQ
FRNCMVTTLCCGKNPLGD---STTVSKTETSQVAPA
>O2D2
sequence:O2D2:1: :308: :1:1
MRQINQTQVTEFLL-----LGLSDGPHTEQ------LLFIVLLGVY--LVTVLG---NLLLISL---VHV
DSQLHTPMYFFLCNLSLADLCFSTNIVPQALV-------HLLSRKKVIAFTLCAARLLFFLIFGCTQCAL
LAVMSY-----------DRYVAICNPLRYPDIMTWKVCVQLATGSWTSGILVSVVDTTFT-LRLPYRGSN
SIAHFFCEAPALLILASTDTHASEMAIFLTGVVILLIPVFLILVSYGR---IIVTVVKMKSTVGSLKAFS
TCGSHLMVVILF------YGSAIITYMTPK-----SSKQQEKSV--------------SVFYAIVTPMLN
PLIYSLR--NKDVKAAL--------RKVATRNF-P-
The log file I got is:
C:\mod6v2\bin>set MODINSTALL6v2=c:\mod6v2
C:\mod6v2\bin>set KEY_MODELLER6v2=$The key i got$
C:\mod6v2\bin>set LIBS_LIB6v2=c:\mod6v2\modlib\libs.lib
C:\mod6v2\bin>set EXECUTABLE_TYPE6v2=i386-windf
C:\mod6v2\bin>set
PATH=c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program
Files\Common Files\Adaptec Shared\System;c:\matlab6p1\bin\win32;C:\Program
Files\SSH Communications Security\SSH Secure
Shell;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin
C:\mod6v2\bin>c:\mod6v2\bin\modeller6v2 model-default.top
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, Windows_NT SETHI x86 Family 15
Model 2 Stepping 7, GenuineIn
Date and time of compilation         : Jul 09 2002 16:21:30
Job starting time (YY/MM/DD HH:MM:SS): 2003/04/07  06:33:47.390
TOP_________>   109  709 SET STARTING_MODEL = 1
TOP_________>   110  710 SET ENDING_MODEL = 3
TOP_________>   111  711 CALL ROUTINE    = 'model'
TOP_________>   112  399 CALL ROUTINE = 'getnames'
TOP_________>   113  509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined',
OPERATION;
                       = 'EQ', THEN =     'STRING_OPERATE OPERATION =
CONCATENA;
                      TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT =
MODEL'
TOP_________>   114  510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined',
OPERATI;
                      ON = 'EQ', THEN =     'STRING_OPERATE OPERATION =
CONCATE;
                      NATE, STRING_ARGUMENTS = SEQUENCE .rsr,  RESULT =
CSRFILE;
                      '
TOP_________>   115  511 STRING_OPERATE OPERATION = 'CONCATENATE',
;
                         STRING_ARGUMENTS = SEQUENCE '.sch',  RESULT =
SCHFILE
TOP_________>   116  512 STRING_OPERATE OPERATION = 'CONCATENATE',
;
                        STRING_ARGUMENTS = SEQUENCE '.mat',  RESULT =
MATRIX_FI;
                      LE
TOP_________>   117  513 SET ROOT_NAME = SEQUENCE
TOP_________>   118  514 RETURN
TOP_________>   119  400 CALL ROUTINE = 'homcsr'
TOP_________>   120  106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES =
KNOWNS SEQUE;
                      NCE
Dynamically allocated memory at         amaxseq [B,kB,MB]:      2560929
2500.907     2.442
openf5__224_> Open       11  OLD  SEQUENTIAL  \mod6v2\alignments/
openf5__228E> Error openning file:  \mod6v2\alignments/
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1
Dynamically allocated memory at          finish [B,kB,MB]:      2560929
2500.907     2.442
Starting time                                            : 2003/04/07
06:33:47.390
Closing time                                             : 2003/04/07
06:33:49.687
Total CPU time [seconds]                                 :       1.92
I dont know whether this is an error of mine or is it that I havent
installed it properly or that my top file is wrong. Could someone please
help me out?
Thank you in advance,
Anurag Sethi

Anurag Sethi

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