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On 16/08/2011 7:04 AM, César Ávila wrote:
<blockquote
cite="mid:CAKz=r7JsHjt3S3K4-oyQf7p2NZQrsSFUC-7_sxw9kfu82RtDfw@mail.gmail.com"
type="cite">I am using the latest vesion of DSSP (the one
available at DSSP homepage)<br>
</blockquote>
<br>
So, as discussed in some thread to which I was referring, there have
been some changes to DSSP that prior versions of GROMACS don't cope
with. Until GROMACS updates, use a version of DSSP that's at least a
year old.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAKz=r7JsHjt3S3K4-oyQf7p2NZQrsSFUC-7_sxw9kfu82RtDfw@mail.gmail.com"
type="cite"><br>
<div class="gmail_quote">2011/8/11 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 bgcolor="#FFFFFF" text="#000000">
<div class="im"> On 10/08/2011 6:03 AM, César Ávila wrote:
<blockquote 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>
</div>
Are you using a version of DSSP that is compatible with
GROMACS, pre previous discussion of DSSP changes?<br>
<font color="#888888"> <br>
Mark</font>
<div>
<div class="h5"><br>
<br>
<blockquote 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"
target="_blank">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/"
target="_blank">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" target="_blank">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"
target="_blank">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>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>
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