-bash-3.00$ editconf -f SWNT_6_6_144.pdb -o SWNT_6_6_144.gro -d 1.0
                         :-)  G  R  O  M  A  C  S  (-:

                          GROtesk MACabre and Sinister

                            :-)  VERSION 3.3.1  (-:


      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2006, 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.

                               :-)  editconf  (-:

Option     Filename  Type         Description
------------------------------------------------------------
  -f SWNT_6_6_144.pdb  Input        Generic structure: gro g96 pdb tpr tpb
                                   tpa xml
  -n      index.ndx  Input, Opt.  Index file
  -o SWNT_6_6_144.gro  Output, Opt! Generic structure: gro g96 pdb xml
-mead      mead.pqr  Output, Opt. Coordinate file for MEAD
 -bf      bfact.dat  Input, Opt.  Generic data 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      0  Set the nicelevel
      -[no]w   bool     no  View output xvg, xpm, eps and pdb files
   -[no]ndef   bool     no  Choose output from default index groups
         -bt   enum triclinic  Box type for -box and -d: triclinic, cubic,
                            dodecahedron or octahedron
        -box vector  0 0 0  Box vector lengths (a,b,c)
     -angles vector 90 90 90  Angles between the box vectors (bc,ac,ab)
          -d   real      1  Distance between the solute and the box
      -[no]c   bool     no  Center molecule in box (implied by -box and -d)
     -center vector  0 0 0  Coordinates of geometrical center
  -translate vector  0 0 0  Translation
     -rotate vector  0 0 0  Rotation around the X, Y and Z axes in degrees
  -[no]princ   bool     no  Orient molecule(s) along their principal axes
      -scale vector  1 1 1  Scaling factor
    -density   real   1000  Density (g/l) of the output box achieved by
                            scaling
    -[no]vol   bool    yes  Compute and print volume of the box
    -[no]pbc   bool     no  Remove the periodicity (make molecule whole
                            again)
  -[no]grasp   bool     no  Store the charge of the atom in the B-factor
                            field and the radius of the atom in the occupancy
                            field
       -rvdw   real   0.12  Default Van der Waals radius (in nm) if one can
                            not be found in the database or if no parameters
                            are present in the topology file
      -sig56   real      0  Use rmin/2 (minimum in the Van der Waals
                            potential) rather than sigma/2 
-[no]vdwread   bool     no  Read the Van der Waals radii from the file
                            vdwradii.dat rather than computing the radii
                            based on the force field
   -[no]atom   bool     no  Force B-factor attachment per atom
 -[no]legend   bool     no  Make B-factor legend
      -label string      A  Add chain label for all residues

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:

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. Eisenberg and A. D. McLachlan
Solvation energy in protein folding and binding
Nature 319 (1986) pp. 199-203
-------- -------- --- Thank You --- -------- --------

Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
WARNING: all CONECT records are ignored
Read 144 atoms
Volume: 0 nm^3, corresponds to roughly 0 electrons
No velocities found
    system size :  0.817  0.817  1.354 (nm)
    center      :  0.000 -0.000 -0.062 (nm)
    box vectors :  0.000  0.000  0.000 (nm)
    box angles  :   0.00   0.00   0.00 (degrees)
    box volume  :   0.00               (nm^3)
    shift       :  1.408  1.408  1.739 (nm)
new center      :  1.408  1.408  1.677 (nm)
new box vectors :  2.817  2.817  3.354 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  :  26.62               (nm^3)

WARNING: No boxtype specified - distance condition applied in each dimension.
If the molecule rotates the actual distance will be smaller. You might want
to use a cubic box instead, or why not try a dodecahedron today?

gcq#95: "Pretend That You're Hercule Poirot" (TeX)