<b>SIMULATION OF LYSOZYME IN WATER USING GROMACS-4.0.5<br></b><br>STEP: TO NEUTRALIZE THE +8 CHARGE WITH 8 CL- MOLECULES<b><br><br><br>COMMAND GIVEN : <br><br>[root@localhost gromacs-4.0.5]# genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8</b><br>
:-) G R O M A C S (-:<br><br> GRoups of Organic Molecules in ACtion for Science<br><br> :-) VERSION 4.0.5 (-:<br><br><br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br>
Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br> Copyright (c) 2001-2008, The GROMACS development team,<br> check out <a href="http://www.gromacs.org/" target="_blank">http://www.gromacs.org</a> for more information.<br>
<br> This program is free software; you can redistribute it and/or<br> modify it under the terms of the GNU General Public License<br> as published by the Free Software Foundation; either version 2<br>
of the License, or (at your option) any later version.<br><br> :-) genion (-:<br><br>Option Filename Type Description<br>------------------------------------------------------------<br>
-s ions.tpr Input Run input file: tpr tpb tpa<br>-table table.xvg Input, Opt. xvgr/xmgr file<br> -n index.ndx Input, Opt. Index file<br> -o 1AKI_solv_ions.gro Output Structure file: gro g96 pdb<br>
-g genion.log Output Log file<br>-pot pot.pdb Output, Opt. Protein data bank file<br> -p topol.top In/Out, Opt! Topology file<br><br>Option Type Value Description<br>------------------------------------------------------<br>
-[no]h bool no Print help info and quit<br>-nice int 19 Set the nicelevel<br>-[no]xvgr bool yes Add specific codes (legends etc.) in the output<br> xvg files for the xmgrace program<br>
-np int 0 Number of positive ions<br>-pname string NA Name of the positive ion<br>-pq int 1 Charge of the positive ion<br>-nn int 8 Number of negative ions<br>
-nname string CL Name of the negative ion<br>-nq int -1 Charge of the negative ion<br>-rmin real 0.6 Minimum distance between ions<br>-[no]random bool yes Use random placement of ions instead of based on<br>
potential. The rmin option should still work<br>-seed int 1993 Seed for random number generator<br>-scale real 0.001 Scaling factor for the potential for -pot<br>-conc real 0 Specify salt concentration (mol/liter). This will<br>
add sufficient ions to reach up to the specified<br> concentration as computed from the volume of the<br> cell in the input tpr file. Overrides the -np and<br>
nn options.<br>-[no]neutral bool no This option will add enough ions to neutralize<br> the system. In combination with the concentration<br> option a neutral system at a given salt<br>
concentration will be generated.<br><br>WARNING: turning of free energy, will use lambda=0<br>Reading file ions.tpr, VERSION 4.0.5 (single precision)<br>Using a coulomb cut-off of 1 nm<br>Will try to add 0 NA ions and 8 CL ions.<br>
Select a continuous group of solvent molecules<br>Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>Group 0 ( System) has 39055 elements<br>Group 1 ( Protein) has 1960 elements<br>
Group 2 ( Protein-H) has 1001 elements<br>Group 3 ( C-alpha) has 129 elements<br>Group 4 ( Backbone) has 387 elements<br>Group 5 ( MainChain) has 517 elements<br>Group 6 (MainChain+Cb) has 634 elements<br>
Group 7 ( MainChain+H) has 646 elements<br>Group 8 ( SideChain) has 1314 elements<br>Group 9 ( SideChain-H) has 484 elements<br>Group 10 ( Prot-Masses) has 1960 elements<br>Group 11 ( Non-Protein) has 37095 elements<br>
Group 12 ( SOL) has 37095 elements<br>Group 13 ( Other) has 37095 elements<br>Select a group: 12<br>Selected 12: 'SOL'<br>Number of (3-atomic) solvent molecules: 12365<br><br>Processing topology<br>
Replacing 12357 solute molecules in topology file (topol.top) by 0 NA and 8 CL ions.<br><br><span style="color:rgb(255,0,0)">Back Off! I just backed up topol.top to ./#topol.top.2#</span><br style="color:rgb(255,0,0)"><span style="color:rgb(255,0,0)">Replacing solvent molecule 1450 (atom 6310) with CL</span><br style="color:rgb(255,0,0)">
<span style="color:rgb(255,0,0)">Replacing solvent molecule 9368 (atom 30064) with CL</span><br style="color:rgb(255,0,0)"><span style="color:rgb(255,0,0)">Replacing solvent molecule 6035 (atom 20065) with CL</span><br style="color:rgb(255,0,0)">
<span style="color:rgb(255,0,0)">Replacing solvent molecule 10461 (atom 33343) with CL</span><br style="color:rgb(255,0,0)"><span style="color:rgb(255,0,0)">Replacing solvent molecule 4117 (atom 14311) with CL</span><br style="color:rgb(255,0,0)">
<span style="color:rgb(255,0,0)">Replacing solvent molecule 1980 (atom 7900) with CL</span><br style="color:rgb(255,0,0)"><span style="color:rgb(255,0,0)">Replacing solvent molecule 4774 (atom 16282) with CL</span><br style="color:rgb(255,0,0)">
<span style="color:rgb(255,0,0)">Replacing solvent molecule 10956 (atom 34828) with CL</span><br><br><u>THE PROBLEM FACED IS</u>:<br>THE REPLACED CL MOLECULES CANNOT BE SEEN IN THE UPDATED TOPOLOGY FILE. PLEASE TELL ME HOW TO ANALYSE IT.