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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists