[gmx-users] Error while using genion

[Justin Lemkul]

On 6/20/13 1:57 PM, Raji Viswanathan wrote:
> I am new Gromacs user and I found Dr. Kerrigan's tutorial on the spider toxin peptide.  I was going through the steps in the tutorial but got stuck with the genion command.  When I am prompted to select a group, I get the error that it is not found.  I tried many different ways of specifying this but still get the same error.  I would appreciate your help.  I am enclosing the output below:
>
>                            GROtesk MACabre and Sinister
>
>                              :-)  VERSION 4.5.5  (-:
>
>          Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
>        Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
>          Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
>             Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
>                  Michael Shirts, Alfons Sijbers, Peter Tieleman,
>
>                 Berk Hess, David van der Spoel, and Erik Lindahl.
>
>         Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>              Copyright (c) 2001-2010, The GROMACS development team at
>          Uppsala University & The Royal Institute of Technology, Sweden.
>              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        ion.tpr  Input        Run input file: tpr tpb tpa
> -table    table.xvg  Input, Opt.  xvgr/xmgr file
>    -n      index.ndx  Input, Opt.  Index file
>    -o   fws-b4em.gro  Output       Structure file: gro g96 pdb etc.
>    -g        ion.log  Output       Log file
> -pot        pot.pdb  Output, Opt. Protein data bank file
>    -p        fws.top  In/Out, Opt! Topology file
>
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -[no]version bool   no      Print version info and quit
> -nice        int    19      Set the nicelevel
> -xvg         enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
> -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    0       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   0.15    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   yes     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.
>
> Reading file ion.tpr, VERSION 4.5.5 (single precision)
> Using a coulomb cut-off of 1 nm
> Will try to add 12 NA ions and 14 CL ions.
> Select a continuous group of solvent molecules
> Group     0 (         System) has 12666 elements
> Group     1 (        Protein) has   495 elements
> Group     2 (      Protein-H) has   257 elements
> Group     3 (        C-alpha) has    35 elements
> Group     4 (       Backbone) has   105 elements
> Group     5 (      MainChain) has   141 elements
> Group     6 (   MainChain+Cb) has   171 elements
> Group     7 (    MainChain+H) has   176 elements
> Group     8 (      SideChain) has   319 elements
> Group     9 (    SideChain-H) has   116 elements
> Group    10 (    Prot-Masses) has   495 elements
> Group    11 (    non-Protein) has 12171 elements
> Group    12 (          Water) has 12171 elements
> Group    13 (            SOL) has 12171 elements
> Group    14 (      non-Water) has   495 elements
> Select a group:   13
> bash: 13: command not found
>
> [9]+  Stopped                 genion -s ion.tpr -o fws-b4em.gro -neutral -conc 0.15 -p fws.top -g ion.log
>

Your shell is interpreting your selection as a command rather than an input file 
stream.  What OS are you running?

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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