With gdb I am getting the following messages
gdb --args do_dssp -f ../0_trajout.xtc -s ../input/replica_0.tpr
-ssdump data.dat -b 170000 -e 180000 -dt 10
GNU gdb (GDB) 7.2-ubuntu
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later
<http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
Para las instrucciones de informe de errores, vea:
<http://www.gnu.org/software/gdb/bugs/>...
Leyendo símbolos desde /usr/local/gromacs/bin/do_dssp...(no se
encontraron símbolos de depuración)hecho.
(gdb) run
Starting program: /usr/local/gromacs/bin/do_dssp -f ../0_trajout.xtc
-s ../input/replica_0.tpr -ssdump data.dat -b 170000 -e 180000 -dt 10
[Depuración de hilo usando libthread_db enabled]
:-) G R O M A C S (-:
Gromacs Runs One Microsecond At Cannonball Speeds
:-) VERSION 4.5.4-dev-20110803-e49fb5a (-:
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
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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/gromacs/bin/do_dssp (-:
Option Filename Type Description
------------------------------------------------------------
-f ../0_trajout.xtc Input Trajectory: xtc trr trj gro g96
pdb cpt
-s ../input/replica_0.tpr Input Structure+mass(db): tpr tpb
tpa gro
g96 pdb
-n index.ndx Input, Opt. Index file
-ssdump data.dat Output, Opt! Generic data file
-map ss.map Input, Lib. File that maps matrix data to colors
-o ss.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 170000 First frame (ps) to read from trajectory
-e time 180000 Last frame (ps) to read from trajectory
-dt time 10 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
Reading file ../input/replica_0.tpr, VERSION 4.5.3 (single precision)
Reading file ../input/replica_0.tpr, VERSION 4.5.3 (single precision)
Program received signal SIGSEGV, Segmentation fault.
0x00007ffff6ae043c in gmx_strcasecmp () from
/usr/local/gromacs/lib/libgmx.so.6
(gdb) bt
#0 0x00007ffff6ae043c in gmx_strcasecmp () from
/usr/local/gromacs/lib/libgmx.so.6
#1 0x00007ffff6ade68f in search_str () from
/usr/local/gromacs/lib/libgmx.so.6
#2 0x00007ffff7b508d4 in bPhobics () from
/usr/local/gromacs/lib/libgmxana.so.6
#3 0x000000000040309a in main ()
2011/3/9 Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
On 10/03/2011 1:36 AM, Justin A. Lemkul wrote:
ZHAO Lina wrote:
Hi,
How do get the percentage of the secondary structure
propensities of residues?
seems dssp none such effect?
The scout.xvg file contains everything you need (in a broad
sense) - number of residues in a given secondary structure
over time. If you need a per-residue breakdown, there is no
Gromacs tool that does that, but the .xpm file contains that
information, so you can write your own script and extract it.
Actually I modified do_dssp in late January to do that. The OP
will need to download the release-4-5-patches version of
src/tools/do_dssp.c and copy it to their normal installation
directory (or compile release-4-5-patches).
Mark
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