[gmx-users] Problem in implementing do_dssp

[Rishikesh Parulekar]

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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