[gmx-users] do_dssp version error

[Mark Abraham]

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
> >>>>>>> --
> >>>>>>> Gromacs Users mailing list
> >>>>>>>
> >>>>>>> * Please search the archive at http://www.gromacs.org/
> >>>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
> >>>>>>>
> >>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>>>>>
> >>>>>>> * For (un)subscribe requests visit
> >>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> >>>>>>> or
> >>>>>>> send a mail to gmx-users-request at gromacs.org.
> >>>>>>>
> >>>>>>> --
> >>>>>>>
> >>>>>> Gromacs Users mailing list
> >>>>>>
> >>>>>> * Please search the archive at http://www.gromacs.org/
> >>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
> >>>>>>
> >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>>>>
> >>>>>> * For (un)subscribe requests visit
> >>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> >>>>>> send a mail to gmx-users-request at gromacs.org.
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>> ==================================================
> >>>>
> >>>> 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
> >>>>
> >>>> ==================================================
> >>>>
> >>>> --
> >>>> Gromacs Users mailing list
> >>>>
> >>>> * Please search the archive at http://www.gromacs.org/Support
> >>>> /Mailing_Lists/GMX-Users_List before posting!
> >>>>
> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>>
> >>>> * For (un)subscribe requests visit
> >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>>> send a mail to gmx-users-request at gromacs.org.
> >>>>
> >>>>
> >>>
> >>>
> > --
> > ==================================================
> >
> > 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
> >
> > ==================================================
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/Support
> > /Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>