Which version of Gromacs?  There was a bug in genbox that was fixed for version 
4.0.4.
-Justin

Ken Rotondi wrote:
Hello All,

I have managed to get urea into the G53a6 ffield with suitable adjustments to the appropriate .pdb, .rtp, and .hdb files. I am trying to use the resulting urea.gro file (I have also tried with a urea.pdb file generated from the urea.gro file using pdb2gmx) in genbox using the -ci flag.
If I run the following steps:

pdb2gmx -f diala.pdb -o diala.gro -p diala.top -ff G53a6 -ignh

editconf -f diala.gro -o dialabox.gro -bt dodecahedron -box 3.1

genbox -cp dialabox.gro -cs spc216.gro -ci urea.gro -nmol 1 -o dialasoln.gro -p diala.top
The first 3 commands execute normally, however the third ends in a seg 
fault (following). I suspect if I was more knowledgeable I would know 
something about setting a breakpoint in malloc_error_break, 
unfortunately this is opaque to me. Any help pointing me in the right 
direction is as always appreciated.
Ken

end of output:

Added 1 molecules (out of 1 requested) of UREA
Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues

Initialising van der waals distances...
Will generate new solvent configuration of 2x2x2 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
    SOL (   3 atoms):  1728 residues
Calculating Overlap...
box_margin = 0.315
Removed 2397 atoms that were outside the box
Neighborsearching with a cut-off of 0.45
Table routines are used for coulomb: FALSE
Table routines are used for vdw:     FALSE
Cut-off's:   NS: 0.45   Coulomb: 0.45   LJ: 0.45
System total charge: 0.000
genbox(20672) malloc: *** mmap(size=4274171904) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
./build.txt: line 9: 20672 Segmentation fault genbox -cp dialabox.gro -cs spc216.gro -ci urea.gro -nmol 1 -o dialasoln.gro -p diala.top


Dr. KS Rotondi
The Departments of Chemistry & Biochemistry and Molecular Biology
The University of Massachusetts - Amherst
815B LGRT
Amherst, MA 01075
k...@chemistry.umass.edu

Phone:    413-545-1591
Fax:        413-545-4490

"If there's a solution, why worry? If there's no solution, why worry?"
    The Dali Lama





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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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