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

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 27 02:43:41 CET 2009

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 
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?



Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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