Hi, <br>I downloaded release-4-5-patches from git. It compiles and installs successfully. Nevertheless I am getting a segmentation fault. <br>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 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 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 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 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></div><div class="h5"><br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br>