[gmx-users] do_dssp version error

Mon Sep 12 18:31:45 CEST 2016

hi mark,

i'm using gromacs 4.65 and dssp version is 2.04.

Where i can download a older dssp version ?

thank you

On Mon, Sep 12, 2016 at 9:52 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Then like Justin said, dssp must be of a version unsuitable for do_dssp,
> e.g. you're using an ancient GROMACS do_dssp and a new version of dssp.
>
> Mark
>
> On Mon, Sep 12, 2016 at 5:15 PM Samith Rathnayake <samithzzz1 at gmail.com>
> wrote:
>
> > located on /usr/local/bin/dssp . thus in my .bashrc i do not set the DSSP
> > environment.
> >
> > On Mon, Sep 12, 2016 at 9:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 9/12/16 11:56 AM, Samith Rathnayake wrote:
> > >
> > >> and now this is what i got when do_dssp run : Fatal error:
> > >> DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)
> > >>
> > >> but dssp binary (NOT do_dssp) directly on a PDB file is working
> > >>
> > >>
> > > This is what I meant in point 2.  $DSSP needs to point to your actual
> > dssp
> > > binary, wherever it is.  Either your environment variable is not set,
> or
> > it
> > > is set incorrectly.
> > >
> > > -Justin
> > >
> > >
> > > On Mon, Sep 12, 2016 at 9:21 PM, Samith Rathnayake <
> samithzzz1 at gmail.com
> > >
> > >> wrote:
> > >>
> > >> 1/ yes it working on pdb
> > >>> 3/dssp-2.04
> > >>>
> > >>> thank you
> > >>>
> > >>> On Mon, Sep 12, 2016 at 8:39 PM, Justin Lemkul <jalemkul at vt.edu>
> > wrote:
> > >>>
> > >>>
> > >>>>
> > >>>> On 9/12/16 11:06 AM, Samith Rathnayake wrote:
> > >>>>
> > >>>> thank you
> > >>>>>
> > >>>>> I really appreciate if anyone can tell me simple and step-by step
> > >>>>> solution
> > >>>>>
> > >>>>>
> > >>>>> There are many things that could be wrong.  Most of the normal
> > >>>> troubleshooting can be found with a simple Google search (that's why
> > we
> > >>>> have an archive!) but I will sum up:
> > >>>>
> > >>>> 1. Run the dssp binary (NOT do_dssp) directly on a PDB file - does
> it
> > >>>> work? This is your biggest indicator as any number of things could
> be
> > >>>> wrong
> > >>>> (binary is not executable, not compatible, etc).
> > >>>> 2. Check that your DSSP environment variable is properly set.
> > >>>> 3. What version of DSSP did you download?  The -ver flag is used by
> > >>>> do_dssp to account for differences in syntax.
> > >>>>
> > >>>> -Justin
> > >>>>
> > >>>>
> > >>>>
> > >>>> thank you
> > >>>>>
> > >>>>>
> > >>>>> regards
> > >>>>>
> > >>>>> samith
> > >>>>>
> > >>>>>
> > >>>>> On Mon, Sep 12, 2016 at 7:09 PM, Sarath Chandra <
> > >>>>> sarathchandradantu at gmail.com> wrote:
> > >>>>>
> > >>>>> dssp by default gets installed as mkdssp.
> > >>>>>
> > >>>>>>
> > >>>>>> Do an export DSSP=path_to_mkdssp_executable
> > >>>>>>
> > >>>>>> and it will worl
> > >>>>>>
> > >>>>>> On 12 September 2016 at 18:01, Samith Rathnayake <
> > >>>>>> samithzzz1 at gmail.com>
> > >>>>>> wrote:
> > >>>>>>
> > >>>>>> Dear all
> > >>>>>>
> > >>>>>>>
> > >>>>>>> When i'm run the do_dssp command in the gromacs
> > >>>>>>>
> > >>>>>>> do_dssp -f ../run01/run01.trr -s ../run01/run01.tpr -sc
> scount.xvg
> > -o
> > >>>>>>> ss.xpm -dt 10 -ver 2
> > >>>>>>>
> > >>>>>>> i got this error
> > >>>>>>>
> > >>>>>>> There are 455 residues in your selected group
> > >>>>>>> dssp cmd='/usr/local/bin/dssp -i dd5J9xcr -o ddPd7b8G > /dev/null
> > 2>
> > >>>>>>> /dev/null'
> > >>>>>>> trn version: GMX_trn_file (single precision)
> > >>>>>>> Reading frame       0 time    0.000
> > >>>>>>> Back Off! I just backed up dd5J9xcr to ./#dd5J9xcr.1#
> > >>>>>>>
> > >>>>>>> -------------------------------------------------------
> > >>>>>>> Program do_dssp, VERSION 4.6.5
> > >>>>>>> Source code file: /home/samith/gromacs-4.6.5/src
> > >>>>>>> /tools/gmx_do_dssp.c,
> > >>>>>>> line:
> > >>>>>>> 669
> > >>>>>>>
> > >>>>>>> Fatal error:
> > >>>>>>> Failed to execute command: Try specifying your dssp version with
> > the
> > >>>>>>> -ver
> > >>>>>>> option.
> > >>>>>>>
> > >>>>>>> For more information and tips for troubleshooting, please check
> the
> > >>>>>>>
> > >>>>>>> GROMACS
> > >>>>>>
> > >>>>>> website at http://www.gromacs.org/Documentation/Errors
> > >>>>>>>
> > >>>>>>> thank you
> > >>>>>>>
> > >>>>>>> regards
> > >>>>>>> samith
> > >>>>>>> --
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> > >>>>>> --
> > >>>> ==================================================
> > >>>>
> > >>>> Justin A. Lemkul, Ph.D.
> > >>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >>>>
> > >>>> Department of Pharmaceutical Sciences
> > >>>> School of Pharmacy
> > >>>> Health Sciences Facility II, Room 629
> > >>>> University of Maryland, Baltimore
> > >>>> 20 Penn St.
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> > >>>>
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> > >>>> http://mackerell.umaryland.edu/~jalemkul
> > >>>>
> > >>>> ==================================================
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> > >>>>
> > >>>>
> > >>>
> > >>>
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 629
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==================================================
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