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 <r...@yu.edu>
Subject: [gmx-users] Error while using genion
To: "gmx-users@gromacs.org" <gmx-users@gromacs.org>
Message-ID:
<b8c111f917e93f4ebb8ff5c751aa91ae431b7...@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
========================================
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