[gmx-users] problem with genbox -ci option

[Ken Rotondi]

Dear Justin, All,

Yes, running as two separate steps works, is this a known genbox bug?

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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>
> -- 
> ========================================
>
> 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
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the www  
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php