[gmx-users] secondary structure propensities of residues

César Ávila clavila at gmail.com
Tue Aug 9 22:03:01 CEST 2011

I downloaded release-4-5-patches from git. It compiles and installs
successfully. Nevertheless I am getting a segmentation fault.
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:
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,
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               Berk Hess, David van der Spoel, and Erik Lindahl.

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                    :-)  /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
                                   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
(gdb) bt
#0  0x00007ffff6ae043c in gmx_strcasecmp () from
#1  0x00007ffff6ade68f in search_str () from
#2  0x00007ffff7b508d4 in bPhobics () from
#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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