[gmx-users] secondary structure propensities of residues
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Aug 16 01:37:37 CEST 2011
On 16/08/2011 7:04 AM, César Ávila wrote:
> I am using the latest vesion of DSSP (the one available at DSSP homepage)
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.
Mark
>
> 2011/8/11 Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto: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
>> <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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>>
>>
>
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