[gmx-users] problem with genbox

[Li, Yun]

Thanks for getting back to me so quickly. I am following this tutorial:
http://www.dddc.ac.cn/embo04/practicals/9_14_1.htm

It seems to be very straight forward. However, I can't overcome my
problem. Here is the output from genbox: 

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

                       GRowing Old MAkes el Chrono Sweat

                            :-)  VERSION 3.1.2  (-:


       Copyright (c) 1991-2002, University of Groningen, The Netherlands
         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.

               :-)  c:\Program Files\Gromacs\bin\genbox.exe  (-:

Option     Filename  Type          Description
------------------------------------------------------------
 -cp        box.pdb  Input, Opt!   Generic structure: gro g96 pdb tpr
tpb tpa
 -cs     spc216.gro  Input, Opt!, Lib.  Generic structure: gro g96 pdb
tpr tpb
                                   tpa
 -ci     insert.gro  Input, Opt.   Generic structure: gro g96 pdb tpr
tpb tpa
  -o      water.pdb  Output        Generic structure: gro g96 pdb
  -p      topol.top  In/Out, Opt!  Topology file

Table routines are used for coulomb: FALSE
Table routines are used for vdw:     FALSE
Cut-off's:   NS: 0.48   Coulomb: 0.48   LJ: 0.48
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 0 molecules, 12298 charge groups and 12298 atoms
There are 0 optimized solvent molecules on node 0
There are 0 optimized water molecules on node 0
Grid: 18 x 14 x 20 cells
Adding line for 2164 solute molecules to topology file (topol.top)
      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

Reading solute configuration
PROTEIN G (B1 IGG-BINDING DOMAIN)
Containing 634 atoms in 80 residues
Initialising van der waals distances...
Opening library file C:\Program Files\Gromacs\share\top\vdwradii.dat
Opening library file C:\Program Files\Gromacs\share\top\aminoacids.dat
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 3x2x3 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
    SOL (   3 atoms):  3888 residues
Calculating Overlap...
box_margin = 0.315
Removed 2868 atoms that were outside the box
Succesfully made neighbourlist
nri = 20556, nrj = 531741
Checking Protein-Solvent overlap: tested 13099 pairs, removed 960 atoms.
Checking Solvent-Solvent overlap: tested 120781 pairs, removed 1416
atoms.
Added 2140 molecules
Generated solvent containing 6420 atoms in 2140 residues
Writing generated configuration to water.pdb

Back Off! I just backed up water.pdb to ./#water.pdb.5#
PROTEIN G (B1 IGG-BINDING DOMAIN)

Output configuration contains 7054 atoms in 2220 residues
WARNING: masses will be determined based on residue and atom names,
         this can deviate from the real mass of the atom type
Opening library file C:\Program Files\Gromacs\share\top\atommass.dat
Volume                 :     75.6474 (nm^3)
Density                :     991.464 (g/l)
Number of SOL molecules:   2164   

Processing topology

Back Off! I just backed up temp.top to ./#temp.top.5#

Back Off! I just backed up topol.top to ./#topol.top.6#

gcq#115: "A Lady Shaves Her Legs" (C. Meijering)


Yun Li
 
Assistant Professor of Chemistry
Delaware Valley College
700 E. Butler Ave.,
Doylestown, PA 18901
(215) 489-2482