[gmx-users] help needed

[Mark Abraham]

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 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 <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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