[gmx-users] Problem in implementing do_dssp

Wed Apr 6 19:08:40 CEST 2016

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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>>>
> --
> ==================================================
>
> 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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