[gmx-users] Problem in implementing do_dssp

Jianguo Li ljggmx at yahoo.com.sg
Thu Apr 7 15:50:55 CEST 2016 

Maybe you could first try chmod +x dssp-2.0.4-linux-i386 , and then do_dssp.
 

    On Thursday, 7 April 2016, 13:45, 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
>> >>>>>>>>>>>> --
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>> >>>>>
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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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