[gmx-users] Problem in implementing do_dssp

[Rishikesh Parulekar]

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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