[gmx-users] Problem in implementing do_dssp

Wed Apr 6 19:26:10 CEST 2016

dssp binaries are those which are obtained from site
ftp://ftp.cmbi.ru.nl/pub/software/dssp ?

On Wed, Apr 6, 2016 at 10:41 PM, Erik Marklund <erik.marklund at chem.ox.ac.uk>
wrote:

> Dear Rishikesh,
>
> No, you misunderstand. We don’t suggest to issue “do_dssp”, but to run
> dssp, which you say is located in /usr/local/bin, to make sure it works the
> way it should.
>
> Kind regards,
> Erik
>
> > On 6 Apr 2016, at 18:08, Rishikesh Parulekar <rishi05parulekar at gmail.com>
> wrote:
> >
> > while running directly it shows do_dssp command not found.
> >
> >
> > On Wed, Apr 6, 2016 at 10:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >>
> >> On 4/6/16 12:57 PM, Rishikesh Parulekar wrote:
> >>
> >>> Hi ErikMarklund,
> >>>        Ya I have tested dssp as it shows all flags options with gmx_mpi
> >>> do_dssp -h that means executable is locatable but it is not giving
> output
> >>> after selecting group protein ends with fatal error : failed to execute
> >>> command. Try specifying your dssp version with the -ver option
> >>>
> >>>
> >> Executing gmx do_dssp is not a valid test of whether or not your dssp
> >> works. That just means your gmx binary is capable of displaying help
> >> information. Please do as Erik and I both suggested and try to run the
> dssp
> >> binary directly, not via gmx do_dssp.
> >>
> >> -Justin
> >>
> >>
> >> On Wed, Apr 6, 2016 at 10:14 PM, Rishikesh Parulekar <
> >>> rishi05parulekar at gmail.com> wrote:
> >>>
> >>> 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
> >>>>>>>>>>>> --
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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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