[gmx-users] Problem in implementing do_dssp

[Rishikesh Parulekar]

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

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
>> >>>>>>> --
>> >>>>>>> Gromacs Users mailing list
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>
>