AMBER Archive (2009)

Subject: Re: [AMBER] AMBER: segmentation fault when running parmchk

From: Jason Swails (
Date: Tue Nov 03 2009 - 14:22:10 CST


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!

On Tue, Nov 3, 2009 at 2:41 PM, Alexander Boncheff <>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

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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