[gmx-users] Segmentation fault with genbox -nmol (version 4.0.3)

David van der Spoel spoel at xray.bmc.uu.se
Tue Jan 27 08:46:35 CET 2009

Justin A. Lemkul wrote:
> Hi All,
> I'm building a system consisting of a protein complex with a few ligands 
> free in solution at the outset of the simulation.  I'm using genbox -ci 
> -nmol to insert the ligands prior to solvation.  I'm using version 4.0.3 
> on a dual-core Intel MacBook.  The following command fails:
> genbox -cp complex_newbox.gro -ci lig.gro -nmol 10
> The command works, however, for values of -nmol < 4.  The command with 
> -nmol 10 works on another machine, an AMD64 Ubuntu box, so this problem 
> appears specific to my Mac.  Using genbox from version 3.3.3 works just 
> fine on the MacBook, and both 4.0.3 and 3.3.3 were built using the same 
> compilers (gcc suite, version 4.0.1).
> The last few lines of genbox.log from -debug 1 are:
> No fcdata or table file name passed, can not read table, can not do 
> bonded interactions
> Going to determine what solvent types we have.
> ...in case that's helpful.  Any ideas why this may have broken, or why 
> it may be specific to my Mac?
> Thanks,
> Justin
please enter a bugzilla for this.

David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

More information about the gromacs.org_gmx-users mailing list