[gmx-users] Problem in implementing do_dssp

[Rishikesh Parulekar]

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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