[gmx-users] problem with genbox -ci option

[Ken Rotondi]

Sorry, vers 4.0.4 here on an intel macbook running OSX.5.5

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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