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