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
>
>
>
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