[gmx-users] Problem in implementing do_dssp

[Erik Marklund]

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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