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On 31/03/2012 6:02 PM, oindrila das wrote:
<blockquote
cite="mid:CAJuD+6QkOGzQQATG7EBWYLmUS4ofcpRe1G=i8GtcOPQEhcu_5w@mail.gmail.com"
type="cite"><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 moz-do-not-send="true"
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.
<br>
</blockquote>
<br>
What do you mean by "cannot be seen"? It can be seen above that
genion is writing a new version of topol.top. Use<br>
<br>
diff topol.top #topol.top.2#<br>
<br>
to see what it has done. Be sure that your input .top matches the
input .tpr on input, which won't be the case if you re-use the
output as input (e.g. by running genion twice).<br>
<br>
Mark<br>
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