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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