-bash-3.00$ genbox -cp SWNT_6_6_144.gro  -cs -o SWNT_6_6_144_b4em.gro -p SWNT_6_6_144.top -maxsol 804
                         :-)  G  R  O  M  A  C  S  (-:

                              S  C  A  M  O  R  G

                            :-)  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.

                                :-)  genbox  (-:

Option     Filename  Type         Description
------------------------------------------------------------
 -cp SWNT_6_6_144.gro  Input, Opt!  Generic structure: gro g96 pdb tpr tpb
                                   tpa xml
 -cs     spc216.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
                                   xml
  -o SWNT_6_6_144_b4em.gro  Output       Generic structure: gro g96 pdb xml
  -p SWNT_6_6_144.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
     -maxsol    int    804  maximum number of solvent molecules to add if
                            they fit in the box. If zero (default) this is
                            ignored

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
Reading solute configuration
(6,6) Nanotube (1,1,6) replication
Containing 144 atoms in 1 residues
Initialising van der waals distances...
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 1746 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
Grid: 12 x 12 x 14 cells
Succesfully made neighbourlist
nri = 10743, nrj = 245439
Checking Protein-Solvent overlap: tested 2698 pairs, removed 219 atoms.
Checking Solvent-Solvent overlap: tested 43565 pairs, removed 807 atoms.
Added 804 molecules
Generated solvent containing 2412 atoms in 804 residues
Writing generated configuration to SWNT_6_6_144_b4em.gro
(6,6) Nanotube (1,1,6) replication

Output configuration contains 2556 atoms in 805 residues
Volume                 :     26.6164 (nm^3)
Density                :     1011.55 (g/l)
Number of SOL molecules:    804   

Processing topology
Adding line for 804 solute molecules to topology file (SWNT_6_6_144.top)

Back Off! I just backed up SWNT_6_6_144.top to ./#SWNT_6_6_144.top.1#

gcq#251: "Get Down In 3D" (George Clinton)