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
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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
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
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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
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daniele bemporad -
Modeller Caretaker