[gmx-users] Problem in implementing do_dssp

Erik Marklund erik.marklund at chem.ox.ac.uk
Wed Apr 6 19:11:53 CEST 2016 

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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