[gmx-users] Problem in implementing do_dssp

Sarath Chandra sarathchandradantu at gmail.com
Wed Apr 6 10:58:24 CEST 2016

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`



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>

> 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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