[gmx-users] Problem in implementing do_dssp
Mark Abraham
mark.j.abraham at gmail.com
Thu Apr 7 13:39:50 CEST 2016
Hi,
Then likely the problem is that your MPI system doesn't permit you to run a
binary from within gmx_mpi. There's no reason to use gmx_mpi other than for
mdrun, so I recommend you compile and use a normal gmx without MPI.
Mark
On Thu, Apr 7, 2016 at 7:45 AM Rishikesh Parulekar <
rishi05parulekar at gmail.com> wrote:
> Hi justin Lemkul
> dssp binary from usr/local/bin is working fine on its own but the command
> it is showing for secondary structure determination is different i.e
> dssp.exe -i 1crn.pdb -o 1crn.dssp that means I am able to get output in
> .dssp format not in .xpm format which is obtained from command : do_dssp -f
> md.trr -s md.tpr -o ss.xpm. Howere with do_dssp module it shows flags
> corresponding to -f and -s options.
> dssp standalone binary is showing the version DSSP 2.0.4.
>
> On Wed, Apr 6, 2016 at 10:56 PM, Rishikesh Parulekar <
> rishi05parulekar at gmail.com> wrote:
>
> > 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
> >> >>>>>>>>>>>> --
> >> >>>>>>>>>>>> Gromacs Users mailing list
> >> >>>>>>>>>>>>
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> >> >>>>>>>>>>>>
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> >> >>>>>>>>>>>>
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> >> >>>>>
> >> >>>>>> posting!
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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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