I copied dssp executible from http://swift.cmbi.ru.nl/gv/dssp/HTML/distrib.html and saved in /usr/local/bin/dssp folder. and run the command /do_dssp -f ions2.trr -s ions2.tpr -na -o dssp.xpm
i am getting the following errors. Please help me to rectify me..and also suggest me in which step i am doing mistake.
om@om-PC /usr/local/gromacs/om
$ /usr/local/bin/./do_dssp -f ions2.trr -s ions2.tpr -na -o dssp.xpm
:-) G R O M A C S (-:
Grunge ROck MAChoS
:-) VERSION 4.5.3 (-:
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.
:-) /usr/local/bin/./do_dssp (-:
Option Filename Type Description
------------------------------------------------------------
-f ions2.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-s ions2.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt. Index file
-ssdump ssdump.dat Output, Opt. Generic data file
-map ss.map Input, Lib. File that maps matrix data to colors
-o dssp.xpm Output X PixMap compatible matrix file
-sc scount.xvg Output xvgr/xmgr file
-a area.xpm Output, Opt. X PixMap compatible matrix file
-ta totarea.xvg Output, Opt. xvgr/xmgr file
-aa averarea.xvg Output, Opt. xvgr/xmgr 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
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-tu enum ps Time unit: fs, ps, ns, us, ms or s
-[no]w bool no View output xvg, xpm, eps and pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-sss string HEBT Secondary structures for structure count
-------------------------------------------------------
Program do_dssp, VERSION 4.5.3
Source code file: statutil.c, line: 819
Invalid command line argument:
-na
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"I'd Like Monday Mornings Better If They Started Later" (Garfield)
Hello.
Remove the -na command. It should work fine.
Best regards.
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