[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?
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
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