[gmx-users] Problem in implementing do_dssp

[Rishikesh Parulekar]

Hi Justin Lemkul,
It works with gmx binary complied with mpi as u can see this is my command
: gmx_mpi do_dssp -f md.trr -s md.tpr -o ss.xpm -sc protein.xvg -ver 2 .
After executing command I am able to select group for dssp calculation but
it ends with fatal error : failed to execute command. Try specifying your
dssp version with the -ver option

On Wed, Apr 6, 2016 at 9:52 PM, Erik Marklund <erik.marklund at chem.ox.ac.uk>
wrote:

> Dear Rishikesh,
>
> And you have tested that your dssp runs properly on your computer? Do you
> run do_dssp from a script? If so, can you please show the script and maybe
> someone spots something?
>
> Kind regards,
> Erik
>
> > On 6 Apr 2016, at 17:03, Rishikesh Parulekar <rishi05parulekar at gmail.com>
> wrote:
> >
> > Hi all,
> > Is there any possible solution for my mentioned problem of do_dssp
> > implementation fatal error.
> >
> > regards
> >
> > On Wed, Apr 6, 2016 at 6:36 PM, Rishikesh Parulekar <
> > rishi05parulekar at gmail.com> wrote:
> >
> >> my error is not regarding the mismatch of name for the software. It has
> >> recognised the software at usr/local/bin but it is showing fatal error
> : failed
> >> to execute command. Try specifying your dssp version with the -ver
> option.
> >> If the problem is with path of software the error of setenv have
> occured.
> >> Hence I have mentioned the ver in the command : gmx_mpi do_dssp -f
> md.trr
> >> -s md.tpr -o ss.xpm -sc protein.xvg -ver 2 but still the same error.
> >>
> >> On Wed, Apr 6, 2016 at 6:32 PM, Rishikesh Parulekar <
> >> rishi05parulekar at gmail.com> wrote:
> >>
> >>> dssp executable is directly downloaded from the
> >>> ftp://ftp.cmbi.ru.nl/pub/software/dssp site and it has ready to use
> >>> executable file for version 2.0.4. So this is the case and it has been
> kept
> >>> under path /usr/local/bin with dssp name.
> >>>
> >>> On Wed, Apr 6, 2016 at 6:17 PM, Sarath Chandra <
> >>> sarathchandradantu at gmail.com> wrote:
> >>>
> >>>> dssp executable generally gets installed as mkdssp.
> >>>>
> >>>> Check if this is the case.
> >>>>
> >>>> Regards,
> >>>>
> >>>> Sarath
> >>>>
> >>>> --
> >>>> Sarath Chandra Dantu, PhD, ELS
> >>>> Room No. 606, New BSBE Building
> >>>> Department of Biosciences and Bioengineering
> >>>> Indian Institute of Technology Bombay
> >>>> Powai Mumbai, 400-076, India
> >>>>
> >>>>
> >>>> On 6 April 2016 at 18:00, Rishikesh Parulekar <
> >>>> rishi05parulekar at gmail.com>
> >>>> wrote:
> >>>>
> >>>>> I have named dssp executable with proper name in usr/local/bin but
> >>>> still
> >>>>> the error persists. I have also shown the path for the dssp with
> >>>> export.
> >>>>>
> >>>>> On Wed, Apr 6, 2016 at 2:27 PM, Sarath Chandra <
> >>>>> sarathchandradantu at gmail.com
> >>>>>> wrote:
> >>>>>
> >>>>>> do_dssp is looking for /usr/local/bin/dssp and if your dssp
> >>>> executable
> >>>>> has
> >>>>>> some other name do_dssp will fail.
> >>>>>>
> >>>>>> Before you run do_dssp you need to set the DSSP variable.
> >>>>>>
> >>>>>> for bash environment do this:
> >>>>>>
> >>>>>> export DSSP=`which dssp-2.0.4-linux-amd64`
> >>>>>>
> >>>>>> Regards,
> >>>>>>
> >>>>>> Sarath
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> Sarath Chandra Dantu, PhD, ELS
> >>>>>> Room No. 606, New BSBE Building
> >>>>>> Department of Biosciences and Bioengineering
> >>>>>> Indian Institute of Technology Bombay
> >>>>>> Powai Mumbai, 400-076, India
> >>>>>>
> >>>>>>
> >>>>>> On 6 April 2016 at 13:16, Rishikesh Parulekar <
> >>>>> rishi05parulekar at gmail.com>
> >>>>>> wrote:
> >>>>>>
> >>>>>>> Hi dear all,
> >>>>>>>
> >>>>>>>     I am trying to analyse the secondary structure of my protein
> >>>> by
> >>>>>> using
> >>>>>>> do_dssp on gromacs-5.1.2. However it consistently showing the fatal
> >>>>>> error:
> >>>>>>> failed to execute command. Try specifying your dssp version with
> >>>> the
> >>>>> -ver
> >>>>>>> option.
> >>>>>>> I am using dssp executable file i.e dssp-2.0.4-linux-amd64 and it
> >>>> has
> >>>>>> been
> >>>>>>> properly placed in /usr/local/bin and also command with -ver
> >>>> option has
> >>>>>>> also been executed
> >>>>>>> gmx_mpi do_dssp -f md.trr -s md.tpr -o ss.xpm -sc protein.xvg -ver
> >>>> 2
> >>>>> but
> >>>>>>> the fatal error still persists. I am actually not getting the valid
> >>>>>>> solution after many executions.
> >>>>>>>
> >>>>>>> Thanks in advance,
> >>>>>>>
> >>>>>>> Rishikesh S. Parulekar
> >>>>>>> Research scholar,
> >>>>>>> Department of Microbiology,
> >>>>>>> Shivaji University,Kolhapur
> >>>>>>> India
> >>>>>>> --
> >>>>>>> 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.
> >>>>>>
> >>>>> --
> >>>>> 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.
> >>>>
> >>>
> >>>
> >>
> > --
> > 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.
>