[gmx-users] Problem in implementing do_dssp

[Rishikesh Parulekar]

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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>>
>>
>