[gmx-users] problem with genbox -ci option

[Justin A. Lemkul]

Ken Rotondi wrote:
> Sorry, vers 4.0.4 here on an intel macbook running OSX.5.5
> 

Does it work if you use -ci to insert your molecule, then in a separate step, 
use -cs to solvate?

-Justin

> On Apr 23, 2009, at 11:06 AM, Justin A. Lemkul wrote:
> 
>>
>> 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
>>> 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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>>
>> -- 
>> ========================================
>>
>> 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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> 
> 

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

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

========================================