[gmx-users] secondary structure propensities of residues

César Ávila clavila at gmail.com
Mon Aug 15 23:04:52 CEST 2011 

I am using the latest vesion of DSSP (the one available at DSSP homepage)

2011/8/11 Mark Abraham <Mark.Abraham at 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.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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>
>
>
>
>
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