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*SIMULATION OF LYSOZYME IN WATER USING GROMACS-4.0.5
*
STEP: TO NEUTRALIZE THE +8 CHARGE WITH 8 CL- MOLECULES*


COMMAND GIVEN :

[root at localhost gromacs-4.0.5]# genion -s ions.tpr -o 1AKI_solv_ions.gro -p
topol.top -pname NA -nname CL -nn 8*
                         :-)  G  R  O  M  A  C  S  (-:

               GRoups of Organic Molecules in ACtion for Science

                            :-)  VERSION 4.0.5  (-:


      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2008, 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.

                                :-)  genion  (-:

Option     Filename  Type         Description
------------------------------------------------------------
  -s       ions.tpr  Input        Run input file: tpr tpb tpa
-table    table.xvg  Input, Opt.  xvgr/xmgr file
  -n      index.ndx  Input, Opt.  Index file
  -o 1AKI_solv_ions.gro  Output       Structure file: gro g96 pdb
  -g     genion.log  Output       Log file
-pot        pot.pdb  Output, Opt. Protein data bank file
  -p      topol.top  In/Out, Opt! Topology file

Option       Type   Value   Description
------------------------------------------------------
-[no]h       bool   no      Print help info and quit
-nice        int    19      Set the nicelevel
-[no]xvgr    bool   yes     Add specific codes (legends etc.) in the output
                            xvg files for the xmgrace program
-np          int    0       Number of positive ions
-pname       string NA      Name of the positive ion
-pq          int    1       Charge of the positive ion
-nn          int    8       Number of negative ions
-nname       string CL      Name of the negative ion
-nq          int    -1      Charge of the negative ion
-rmin        real   0.6     Minimum distance between ions
-[no]random  bool   yes     Use random placement of ions instead of based on
                            potential. The rmin option should still work
-seed        int    1993    Seed for random number generator
-scale       real   0.001   Scaling factor for the potential for -pot
-conc        real   0       Specify salt concentration (mol/liter). This
will
                            add sufficient ions to reach up to the specified
                            concentration as computed from the volume of the
                            cell in the input tpr file. Overrides the -np
and
                            nn options.
-[no]neutral bool   no      This option will add enough ions to neutralize
                            the system. In combination with the
concentration
                            option a neutral system at a given salt
                            concentration will be generated.

WARNING: turning of free energy, will use lambda=0
Reading file ions.tpr, VERSION 4.0.5 (single precision)
Using a coulomb cut-off of 1 nm
Will try to add 0 NA ions and 8 CL ions.
Select a continuous group of solvent molecules
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Group     0 (      System) has 39055 elements
Group     1 (     Protein) has  1960 elements
Group     2 (   Protein-H) has  1001 elements
Group     3 (     C-alpha) has   129 elements
Group     4 (    Backbone) has   387 elements
Group     5 (   MainChain) has   517 elements
Group     6 (MainChain+Cb) has   634 elements
Group     7 ( MainChain+H) has   646 elements
Group     8 (   SideChain) has  1314 elements
Group     9 ( SideChain-H) has   484 elements
Group    10 ( Prot-Masses) has  1960 elements
Group    11 ( Non-Protein) has 37095 elements
Group    12 (         SOL) has 37095 elements
Group    13 (       Other) has 37095 elements
Select a group: 12
Selected 12: 'SOL'
Number of (3-atomic) solvent molecules: 12365

Processing topology
Replacing 12357 solute molecules in topology file (topol.top)  by 0 NA and
8 CL ions.

Back Off! I just backed up topol.top to ./#topol.top.2#
Replacing solvent molecule 1450 (atom 6310) with CL
Replacing solvent molecule 9368 (atom 30064) with CL
Replacing solvent molecule 6035 (atom 20065) with CL
Replacing solvent molecule 10461 (atom 33343) with CL
Replacing solvent molecule 4117 (atom 14311) with CL
Replacing solvent molecule 1980 (atom 7900) with CL
Replacing solvent molecule 4774 (atom 16282) with CL
Replacing solvent molecule 10956 (atom 34828) with CL

*THE PROBLEM FACED IS*:
THE REPLACED CL MOLECULES CANNOT BE SEEN IN THE UPDATED TOPOLOGY FILE.
PLEASE TELL ME HOW TO ANALYSE IT.
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