So I finally figured out how to debug using gdb.
(gdb) run -i /file.pdb -f pdb -o /file.frcmod
Starting program: /amber10/bin/parmchk -i /file.pdb -f pdb -o /file.frcmod -p $AMBERHOME/dat/leap/parm/parm99.dat
Program received signal SIGSEGV, Segmentation fault.
0x0000000000414a26 in rprepi ()
(gdb)
Any ideas?
----- Original Message -----
From: "Alexander Boncheff" <abonchef.uoguelph.ca>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Tuesday, November 3, 2009 5:29:00 PM GMT -05:00 US/Canada Eastern
Subject: Re: [AMBER] AMBER: segmentation fault when running parmchk
Hi,
I tried adding the -p to the execution command. Still the same results. I've reinstalled gcc and recompiled/installed AmberTools about 3 times, each time the tests pass, and each time I get the segmentation error.
- Alex
----- Original Message -----
From: "Jason Swails" <jason.swails.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Tuesday, November 3, 2009 3:22:10 PM GMT -05:00 US/Canada Eastern
Subject: Re: [AMBER] AMBER: segmentation fault when running parmchk
Hello,
Did you try specifying -p $AMBERHOME/dat/leap/parm/parm99.dat so that it
pulls the parameters from the parm99.dat parameter database? By default it
appears to pull gaff parameters, and I find it unlikely that the atoms are
named properly for gaff.dat. (but maybe this does not matter? a parmchk
expert would be able to say).
Also, do all of your tests pass?
Good luck!
Jason
On Tue, Nov 3, 2009 at 2:41 PM, Alexander Boncheff <abonchef.uoguelph.ca>wrote:
> Dear AMBER users,
>
> Whenever I use parmchk, either for a lib or pdb or prep file I always get a
> Segmentation fault error. Below is what the command line tells me.
>
> ~amber10/exe$ ./parmchk -i file.pdb -f pdb -o file.frcmod
> Segmentation fault (core dumped)
>
> My system is running AMBER10 with AMBERTools 1.2 on Ubuntu 9.10. There is
> one instance in 2004 where another user had a similar error. They were told
> to upload the jmins0.prep file. When I use locate jmins0.prep, nothing is
> found.
>
> Best Regards,
>
> Alex Boncheff
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Nov 04 2009 - 08:30:03 PST
