[gmx-users] Problem in implementing do_dssp

[Sarath Chandra]

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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