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On 10/08/2011 6:03 AM, César Ávila wrote:
<blockquote
cite="mid:CAKz=r7LkKDuRbQiJ4EacOe=pMncYOab6427Lah=BMGfaOjLsBQ@mail.gmail.com"
type="cite">Hi, <br>
I downloaded release-4-5-patches from git. It compiles and
installs successfully. Nevertheless I am getting a segmentation
fault. <br>
</blockquote>
<br>
Are you using a version of DSSP that is compatible with GROMACS, pre
previous discussion of DSSP changes?<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAKz=r7LkKDuRbQiJ4EacOe=pMncYOab6427Lah=BMGfaOjLsBQ@mail.gmail.com"
type="cite">With gdb I am getting the following messages<br>
<br>
<br>
gdb --args do_dssp -f ../0_trajout.xtc -s ../input/replica_0.tpr
-ssdump data.dat -b 170000 -e 180000 -dt 10<br>
GNU gdb (GDB) 7.2-ubuntu<br>
Copyright (C) 2010 Free Software Foundation, Inc.<br>
License GPLv3+: GNU GPL version 3 or later <<a
moz-do-not-send="true" href="http://gnu.org/licenses/gpl.html">http://gnu.org/licenses/gpl.html</a>><br>
This is free software: you are free to change and redistribute it.<br>
There is NO WARRANTY, to the extent permitted by law. Type "show
copying"<br>
and "show warranty" for details.<br>
This GDB was configured as "x86_64-linux-gnu".<br>
Para las instrucciones de informe de errores, vea:<br>
<<a moz-do-not-send="true"
href="http://www.gnu.org/software/gdb/bugs/">http://www.gnu.org/software/gdb/bugs/</a>>...<br>
Leyendo símbolos desde /usr/local/gromacs/bin/do_dssp...(no se
encontraron símbolos de depuración)hecho.<br>
(gdb) run<br>
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<br>
[Depuración de hilo usando libthread_db enabled]<br>
:-) G R O M A C S (-:<br>
<br>
Gromacs Runs One Microsecond At Cannonball Speeds<br>
<br>
:-) VERSION 4.5.4-dev-20110803-e49fb5a (-:<br>
<br>
Written by Emile Apol, Rossen Apostolov, Herman J.C.
Berendsen,<br>
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton
Feenstra, <br>
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter
Meulenhoff, <br>
Teemu Murtola, Szilard Pall, Sander Pronk, Roland
Schulz, <br>
Michael Shirts, Alfons Sijbers, Peter Tieleman,<br>
<br>
Berk Hess, David van der Spoel, and Erik Lindahl.<br>
<br>
Copyright (c) 1991-2000, University of Groningen, The
Netherlands.<br>
Copyright (c) 2001-2010, The GROMACS development team
at<br>
Uppsala University & The Royal Institute of
Technology, Sweden.<br>
check out <a moz-do-not-send="true"
href="http://www.gromacs.org">http://www.gromacs.org</a> for
more information.<br>
<br>
This program is free software; you can redistribute it
and/or<br>
modify it under the terms of the GNU General Public
License<br>
as published by the Free Software Foundation; either
version 2<br>
of the License, or (at your option) any later
version.<br>
<br>
:-) /usr/local/gromacs/bin/do_dssp (-:<br>
<br>
Option Filename Type Description<br>
------------------------------------------------------------<br>
-f ../0_trajout.xtc Input Trajectory: xtc trr trj gro
g96 pdb cpt<br>
-s ../input/replica_0.tpr Input Structure+mass(db): tpr
tpb tpa gro<br>
g96 pdb<br>
-n index.ndx Input, Opt. Index file<br>
-ssdump data.dat Output, Opt! Generic data file<br>
-map ss.map Input, Lib. File that maps matrix data to
colors<br>
-o ss.xpm Output X PixMap compatible matrix file<br>
-sc scount.xvg Output xvgr/xmgr file<br>
-a area.xpm Output, Opt. X PixMap compatible matrix file<br>
-ta totarea.xvg Output, Opt. xvgr/xmgr file<br>
-aa averarea.xvg Output, Opt. xvgr/xmgr file<br>
<br>
Option Type Value Description<br>
------------------------------------------------------<br>
-[no]h bool no Print help info and quit<br>
-[no]version bool no Print version info and quit<br>
-nice int 19 Set the nicelevel<br>
-b time 170000 First frame (ps) to read from
trajectory<br>
-e time 180000 Last frame (ps) to read from
trajectory<br>
-dt time 10 Only use frame when t MOD dt = first
time (ps)<br>
-tu enum ps Time unit: fs, ps, ns, us, ms or s<br>
-[no]w bool no View output .xvg, .xpm, .eps and .pdb
files<br>
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or
none<br>
-sss string HEBT Secondary structures for structure
count<br>
<br>
Reading file ../input/replica_0.tpr, VERSION 4.5.3 (single
precision)<br>
Reading file ../input/replica_0.tpr, VERSION 4.5.3 (single
precision)<br>
<br>
Program received signal SIGSEGV, Segmentation fault.<br>
0x00007ffff6ae043c in gmx_strcasecmp () from
/usr/local/gromacs/lib/libgmx.so.6<br>
(gdb) bt<br>
#0 0x00007ffff6ae043c in gmx_strcasecmp () from
/usr/local/gromacs/lib/libgmx.so.6<br>
#1 0x00007ffff6ade68f in search_str () from
/usr/local/gromacs/lib/libgmx.so.6<br>
#2 0x00007ffff7b508d4 in bPhobics () from
/usr/local/gromacs/lib/libgmxana.so.6<br>
#3 0x000000000040309a in main ()<br>
<br>
<br>
<div class="gmail_quote">
2011/3/9 Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im">On 10/03/2011 1:36 AM, Justin A. Lemkul wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
ZHAO Lina wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
How do get the percentage of the secondary structure
propensities of residues?<br>
<br>
seems dssp none such effect?<br>
<br>
</blockquote>
<br>
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.<br>
</blockquote>
<br>
</div>
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).<br>
<font color="#888888">
<br>
Mark</font>
<div>
<div class="h5"><br>
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</blockquote>
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