[gmx-users] problem with genbox -ci option

Ken Rotondi ksr at chemistry.umass.edu
Thu Apr 23 16:37:33 CEST 2009

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.


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  

Dr. KS Rotondi
The Departments of Chemistry & Biochemistry and Molecular Biology
The University of Massachusetts - Amherst
Amherst, MA 01075
ksr at 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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