[gmx-users] secondary structure propensities of residues
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Aug 11 11:53:31 CEST 2011
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.Abraham at anu.edu.au
> <mailto:Mark.Abraham at 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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