[gmx-users] Problem with genbox

Mark Zottola mzottola at gmail.com
Mon Jul 16 04:53:01 CEST 2007

I am trying to run genbox and am getting a segmentation fault.  After
running pdg2gmx, I generated a gro file from the pdb outfput from pdb2gmx
using editconf.  I then ran the editconf which seemed to run without
problem.  Then I tried to use genbox.  It was at this point I received a
segmentation fault.  I have attached the log file from genbox.

As I am new user to Gromacs, I am trying to follow the spider toxin tutorial
for my protein.  Any hints or pointers would be welcome.


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                         :-)  G  R  O  M  A  C  S  (-:

               Go Rough, Oppose Many Angry Chinese Serial killers

                            :-)  VERSION 3.2.1  (-:

      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2004, The GROMACS development team,
            check out http://www.gromacs.org for more information.

         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

                :-)  /opt/asn/apps/gromacs_3.2.1/gromacs-3.2.1/x86_64-unknown-linux-gnu/bin/genbox_mpi_d (double precision)  (-:

Option     Filename  Type         Description
 -cp        gmx.pdb  Input, Opt!  Generic structure: gro g96 pdb tpr tpb tpa
 -cs        gmx.gro  Input, Opt!, Lib. Generic structure: gro g96 pdb tpr tpb
                                   tpa xml
 -ci     insert.gro  Input, Opt.  Generic structure: gro g96 pdb tpr tpb tpa
  -o        gmx.pdb  Output       Generic structure: gro g96 pdb xml
  -p        gmx.top  In/Out, Opt! Topology file

      Option   Type  Value  Description
      -[no]h   bool     no  Print help info and quit
      -[no]X   bool     no  Use dialog box GUI to edit command line options
       -nice    int     19  Set the nicelevel
        -box vector  0 0 0  box size
       -nmol    int      0  no of extra molecules to insert
        -try    int     10  try inserting -nmol*-try times
       -seed    int   1997  random generator seed
       -vdwd   real  0.105  default vdwaals distance
      -shell   real      0  thickness of optional water layer around solute

WARNING: masses will be determined based on residue and atom names,
         this can deviate from the real mass of the atom type
In case you use free energy of solvation predictions:

D. Eisenberg and A. D. McLachlan
Solvation energy in protein folding and binding
Nature 319 (1986) pp. 199-203
-------- -------- --- Thank You --- -------- --------

Opening library file /opt/asn/apps/gromacs_3.2.1/gromacs-3.2.1/share/top/aminoacids.dat
Opening library file /opt/asn/apps/gromacs_3.2.1/gromacs-3.2.1/share/top/atommass.dat
Opening library file /opt/asn/apps/gromacs_3.2.1/gromacs-3.2.1/share/top/vdwradii.dat
Opening library file /opt/asn/apps/gromacs_3.2.1/gromacs-3.2.1/share/top/dgsolv.dat
Reading solute configuration
GROningen Mixture of Alchemy and Childrens' Stories
Containing 2998 atoms in 293 residues
Initialising van der waals distances...
Reading solvent configuration
"GROningen Mixture of Alchemy and Childrens' Stories"
solvent configuration contains 2998 atoms in 293 residues

Initialising van der waals distances...
Will generate new solvent configuration of 2x2x2 boxes
Generating configuration
Sorting configuration
Found 20 different molecule types:
    VAL (  10 atoms):   200 residues
    HIS (  12 atoms):    64 residues
    GLN (  12 atoms):    48 residues
    LEU (   9 atoms):   200 residues
    TYR (  18 atoms):    88 residues
    ARG (  17 atoms):   160 residues
    ALA (   6 atoms):   184 residues
    SER (   8 atoms):   168 residues
    THR (   9 atoms):   104 residues
    LYS (  13 atoms):   120 residues
    TRP (  21 atoms):    64 residues
    GLU (  10 atoms):   176 residues
    GLY (   5 atoms):   200 residues
    PRO (   7 atoms):   144 residues
    ASP (   9 atoms):   120 residues
    PHE (  17 atoms):   120 residues
    ILE (   9 atoms):    56 residues
    CYS (   8 atoms):    32 residues
    MET (   9 atoms):    40 residues
    ASN (  11 atoms):    56 residues

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