[gmx-users] Simulation in octanol as solvent

nur avneet nuravneet at yahoo.co.in
Thu Mar 15 07:45:55 CET 2007

Dear All..
 i want to add octanol as solvent...bt everytime i give genbox command it says 0 solvent molecules added.
 I got the octanol equilibrated box from gromacs contributors section. it was of ffooplsa type...when i changed the atom types and topology through prodrg...the same problem persists.
 bash-3.00# /usr/local/gromacs/bin/genbox -cp kif1g_md_box_oct.gro -cs octanol512.gro -o kif1g_md_oct.gro -p kif1g.top
                          :-)  G  R  O  M  A  C  S  (-:
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       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.
                     :-)  /usr/local/gromacs/bin/genbox  (-:
 Option     Filename  Type         Description
  -cp kif1g_md_box_oct.gro  Input, Opt!  Generic structure: gro g96 pdb tpr
                                    tpb tpa xml
  -cs octanol512.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 kif1g_md_oct.gro  Output       Generic structure: gro g96 pdb xml
   -p      kif1g.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      0  maximum number of solvent molecules to add if
                             they fit in the box. If zero (default) this is
 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 /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
 Containing 68 atoms in 1 residues
 Initialising van der waals distances...
 Reading solvent configuration
 "OcOH Pure Solvent"
 solvent configuration contains 13824 atoms in 512 residues
 Initialising van der waals distances...
 Will generate new solvent configuration of 1x1x1 boxes
 Generating configuration
 Sorting configuration
 Found 1 molecule type:
    OcOH (  27 atoms):   512 residues
 Calculating Overlap...
 box_margin = 0.45
 Removed 7155 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: 17 x 17 x 17 cells
 Succesfully made neighbourlist
 nri = 23737, nrj = 792271
 Checking Protein-Solvent overlap: tested 941 pairs, removed 378 atoms.
 Checking Solvent-Solvent overlap: tested 32848 pairs, removed 2187 atoms.
 Added 152 molecules
 Generated solvent containing 4104 atoms in 152 residues
 Writing generated configuration to kif1g_md_oct.gro
 Back Off! I just backed up kif1g_md_oct.gro to ./#kif1g_md_oct.gro.2#
 Output configuration contains 4172 atoms in 153 residues
 Volume                 :     58.7777 (nm^3)
 Density                :      541.15 (g/l)
 Number of SOL molecules:      0
 Please guide...wheres the problem....
 Here’s a new way to find what you're looking for - Yahoo! Answers 
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