I am using the latest vesion of DSSP (the one available at DSSP homepage) 2011/8/11 Mark Abraham <mark.abra...@anu.edu.au>
> On 10/08/2011 6:03 AM, César Ávila wrote: > > Hi, > I downloaded release-4-5-patches from git. It compiles and installs > successfully. Nevertheless I am getting a segmentation fault. > > > Are you using a version of DSSP that is compatible with GROMACS, pre > previous discussion of DSSP changes? > > Mark > > > 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 > 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/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> > >> 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 >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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