core dumped when reading my restraint file
Hi all When in my .top file I include: # Redefine the rd_restraints routine: SUBROUTINE ROUTINE = 'rd_restraints' # This is the default homology-derived restraints: READ_RESTRAINTS FILE = CSRFILE , ADD_RESTRAINTS = off # This is the additional user provided file: READ_RESTRAINTS FILE = 'my_restraint.rsr' , ADD_RESTRAINTS = on SET ADD_RESTRAINTS = off RETURN END_SUBROUTINE modeller dies with no message and dumps a core. It seems to read my_restraint.rsr , because if I introduce mistakes in the format they are recognised and also because the lines in my_restraint.rsr are present in the core file. I tried to locate: READ_RESTRAINTS FILE = 'my_restraint.rsr' , ADD_RESTRAINTS = on into the "special_restraints" subroutine, but the result is still that modeller dies and dumps a core. I have noticed that if I write "READ_RESTRAINTS FILE = 'my_restraint.rsr' " without "ADD_RESTRAINTS = on" then everything works fine. But as far as I understand the program, this would make modeller forget about the homology-derived restraints, wouldn't it ? Am I making some stupid mistake ? Is there a problem with my compilation or with this version of the program ? Any help is greatly appreciated. Many thanks Daniele __________________________________ Do you Yahoo!? Vote for the stars of Yahoo!'s next ad campaign! http://advision.webevents.yahoo.com/yahoo/votelifeengine/
In order to diagnose this problem, send me your restraints file. I will also need to know which version of Modeller you're using, and on which machine type (e.g. Windows, Sun). Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mailing list: http://salilab.org/mailman/listinfo/modeller_usage
Hi Many thanks for your reply. My restraint file looks like: MODELLER5 VERSION: MODELLER FORMAT R 3 1 1 27 2 2 0 3077 3088 6.5977 0.1000 R 3 1 1 27 2 2 0 3077 3089 7.7258 0.1000 R 3 1 1 27 2 2 0 3077 3093 8.8338 0.1000 and so on, for a total of 10512 lines (but if I use only a few the problem still exists). All lines end with the "newline" character. I'm using modeller6v2 on a linux PC with pentium processor (RedHat 7.2). Just to be clear: I have made sure that my distance restraints don't collide with the homology-derived ones. Daniele --- Modeller Caretaker <modeller-care@salilab.org> wrote: > In order to diagnose this problem, send me your > restraints file. I will > also need to know which version of Modeller you're > using, and on which > machine type (e.g. Windows, Sun). > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org > http://www.salilab.org/modeller/ > Modeller mailing list: > http://salilab.org/mailman/listinfo/modeller_usage __________________________________ Do you Yahoo!? New and Improved Yahoo! Mail - 100MB free storage! http://promotions.yahoo.com/new_mail
On Wed, Jul 21, 2004 at 01:40:39AM -0700, daniele bemporad wrote: > Many thanks for your reply. My restraint file looks > like: > MODELLER5 VERSION: MODELLER FORMAT > R 3 1 1 27 2 2 0 3077 3088 > 6.5977 0.1000 > R 3 1 1 27 2 2 0 3077 3089 > 7.7258 0.1000 > R 3 1 1 27 2 2 0 3077 3093 > 8.8338 0.1000 I'm assuming your mail client has wrapped those lines - each 'R' line should be a single line, not two. > Just to be clear: I have made sure that my distance restraints > don't collide with the homology-derived ones. That shouldn't be an issue - at least, such an overlap shouldn't make Modeller crash - at worst, you'll get a poorly optimized solution. Please send all of the necessary inputs to me at modeller-care@salilab.org, and I'll take a look. It is extremely hard to diagnose your problem unless I can reproduce it in the lab. Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mailing list: http://salilab.org/mailman/listinfo/modeller_usage
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daniele bemporad -
Modeller Caretaker