[gmx-users] Error while using genion

[Justin Lemkul]

Please do not reply to the entire digest.  It gets hopelessly confusing.

On 6/24/13 10:51 AM, Raji Viswanathan wrote:
> I am using Red Hat Enterprise Linux 5.5
> Raji

Something about your shell environment is probably hosed.  Do other commands 
that prompt for interactive input work, or just genion?  Does the following work?

echo 13 | genion -s ion.tpr -o fws-b4em.gro -neutral -conc 0.15 -p fws.top -g 
ion.log

-Justin

<snip>

>> Message: 2
>> Date: Thu, 20 Jun 2013 17:57:28 +0000
>> From: Raji Viswanathan <raji at yu.edu>
>> Subject: [gmx-users] Error while using genion
>> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
>> Message-ID:
>> <B8C111F917E93F4EBB8FF5C751AA91AE431B7979 at AEWEXCPM14.yuad.uds.yu.edu>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> 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, P?r 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
>>

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

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

========================================