[gmx-users] problem with genbox -ci option

[Justin A. Lemkul]

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

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