[gmx-users] Error while using genion

Raji Viswanathan raji at yu.edu
Thu Jun 20 19:57:28 CEST 2013

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

More information about the gromacs.org_gmx-users mailing list