[gmx-users] problem with genbox -ci option

Ken Rotondi ksr at chemistry.umass.edu
Thu Apr 23 19:35:06 CEST 2009 

Indeed this seems likely. I was able to add 125 urea and solvate w/out  
incident doing it in two steps.

Thanks again,

Ken

On Apr 23, 2009, at 1:31 PM, Justin A. Lemkul wrote:

>
>
> Ken Rotondi wrote:
>> Dear Justin, All,
>> Yes, running as two separate steps works, is this a known genbox bug?
>
> I don't know that it's a bug per se, more of a limitation.  The  
> program is trying to solvate the structure, as well as cram in X  
> molecules of something else all at once and probably gets confused.
>
> -Justin
>
>> Ken
>> -works-
>> 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 -ci urea.gro -nmol 1 -o dialaurea.gro -p  
>> diala.top
>> genbox -cp dialaurea.gro -cs spc216.gro -o dialaureasoln.gro -p  
>> diala.top
>> On Apr 23, 2009, at 12:57 PM, Justin A. Lemkul wrote:
>>>
>>>
>>> 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
>>>>>
>>>>> ========================================
>>>>> _______________________________________________
>>>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>>> Please search the archive at http://www.gromacs.org/search  
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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
>>>
>>> ========================================
>>> _______________________________________________
>>> gmx-users mailing list    gmx-users at gromacs.org
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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
>
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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