Hi,

You haven't said anything about the alignment file, seqalin.ali. You should have this file in the same directory where you have placed the .top file

raghu

On Mon, 7 Mar 2005, rathankar rao wrote:

> Dear sir > i have just started using modeller7v7 but have landed in to some problems.i have a few doubts > 1. which directory should i place the top files, ali files and the pdb files. i placed top files in the bin, pdb files in atom-files directory. and tried to run the command, but it shows this error > > > MODELLER 7v7, Sep 12, 2004 09:15pm > PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS > > Copyright(c) 1989-2004 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, 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, Win2000 build 2195 Service Pack 4, PROJECTBT, uni, x86 Family 15 Model 2 Stepping 9 > Date and time of compilation : 09/13/2004 17:17:22 > Job starting time (YY/MM/DD HH:MM:SS): 2004/12/27 13:26:51.093 > TOP_________> 109 749 SET ALNFILE = 'seqalin.ali' > > TOP_________> 110 750 SET KNOWNS = '1ocs' > > TOP_________> 111 751 SET SEQUENCE = 'yhr' > > TOP_________> 112 752 SET ATOM_FILES_DIRECTORY = './:../atom_files' > > TOP_________> 113 753 SET STARTING_MODEL = 1 > > TOP_________> 114 754 SET ENDING_MODEL = 1 > > TOP_________> 115 755 CALL ROUTINE = 'model' > > TOP_________> 116 419 CALL ROUTINE = 'getnames' > > TOP_________> 117 534 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; > = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; > TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' > > TOP_________> 118 535 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; > ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; > NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; > ' > > TOP_________> 119 536 STRING_OPERATE OPERATION = 'CONCATENATE', ; > STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE > > TOP_________> 120 537 STRING_OPERATE OPERATION = 'CONCATENATE', ; > STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; > LE > > TOP_________> 121 538 SET ROOT_NAME = SEQUENCE > > TOP_________> 122 539 RETURN > > TOP_________> 123 420 CALL ROUTINE = 'homcsr' > > TOP_________> 124 112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; > NCE > > Dynamically allocated memory at amaxseq [B,kB,MB]: 84067 82.097 0.080 > fullfn__230E> File not found: seqalin.ali > Directories: > Extensions : :.ali > Prefixes : nothing, pdb > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > Dynamically allocated memory at finish [B,kB,MB]: 84067 82.097 0.080 > Starting time : 2004/12/27 13:26:51.093 > Closing time : 2004/12/27 13:26:52.078 > Total CPU time [seconds] : 0.97 > > > > --------------------------------- > Celebrate Yahoo!'s 10th Birthday! > Yahoo! Netrospective: 100 Moments of the Web