On 31/03/2012 6:02 PM, oindrila das wrote:
*SIMULATION OF LYSOZYME IN WATER USING GROMACS-4.0.5
*
STEP: TO NEUTRALIZE THE +8 CHARGE WITH 8 CL- MOLECULES*
COMMAND GIVEN :
[root@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 <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.
What do you mean by "cannot be seen"? It can be seen above that genion
is writing a new version of topol.top. Use
diff topol.top #topol.top.2#
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).
Mark
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