[gmx-users] problem with genbox -ci option

[Justin A. Lemkul]

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
>>>>> _______________________________________________
>>>>> 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 thewww 
>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>
>>>> -- 
>>>> ========================================
>>>>
>>>> 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
>>
>> -- 
>> ========================================
>>
>> 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
> 
> 

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

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

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