AMBER Archive (2009)

Subject: [AMBER] addles segmentation fault

From: gmail (heptoking_at_gmail.com)
Date: Mon Mar 09 2009 - 03:28:56 CDT

Dear Amber users
     I am trying to do some nudged elastic banding simulation on a big protein (548 residues).
I just went through this by reading the NEB tutorial, which is quite informative and helpful.
(Many thanks to Dr. Ross Walker)
     However, when I used addles to create 30 copies of my protein. The output file said
  Checking topology sizes against compiled limits
 exceeded MAXANG in SIZE.BLOCK.
 MAXANG = 8000
 ntheth = 9788
 exceeded MAXDIH in SIZE.BLOCK.
 MAXDIH = 15000
 nphih = 18572
 Change SIZE.BLOCK and recompile.

I searched the mailing list and found the SIZE.h file and increased these values to 10000 and 20000 respectively to fit my protein.

after make clean,
and make in the $AMBERHOME/src/addles/ folder
I created a new addles program in this folder.


But when I used this command in this folder to create the prmtop and inpcrd file.
There came a segmentation fault

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
addles 08051E1A Unknown Unknown Unknown
addles 0804CD72 Unknown Unknown Unknown
addles 08049B95 Unknown Unknown Unknown
libc.so.6 0076EE33 Unknown Unknown Unknown
addles 08049AD1 Unknown Unknown Unknown

The input and output files are attached.

I really don't know the reason for this.


Please give some suggestions.


Best Regards!

Xiaonan Zhang

Shanghai Public Health Clinical Center




  • application/octet-stream attachment: addles.in

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