[gmx-users] Using do_dssp with GROMACS 4.6.7.

Agnivo Gosai agnivogromacs14 at gmail.com
Fri Jan 30 03:16:32 CET 2015

Dear Users

I want to calculate the secondary structure stability by using DSSP in
GROMACS 4.6.7.
These are the commands that I used for the same :-

(1) ./dssp-2.0.4-linux-i386  ( I am running the DSSP executable )

(2) source /usr/local/gromacs/bin/GMXRC (sourcing GROMACS from my terminal)

(3) export DSSP=/home/upamanyu/Desktop/GROMACS (exporting the path to the
DSSP executable , it is located tin the folder GROMACS)

 (4) do_dssp_467 -s pull1.tpr -f pull1_noPBC.xtc -ver 2

I am able to select the group protein at this stage. Then on hitting enter
this error comes.

Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver

 (5) do_dssp_467 -s pull1.tpr -f pull1_noPBC.xtc -ver 1

Same error comes

 (6)  do_dssp_467 -s pull1.tpr -f pull1_noPBC.xtc

Same error comes

 (7) do_dssp_467 -s pull1.tpr -f pull1_noPBC.xtc -ver 2.0.4

Same error comes

 (8)  ./dssp-2.0.4-linux-i386 -i pull1.pdb -o pull1.dssp

This works fine. But I want to use GROMACS to generate plots and figures
with its do_dssp command.

Kindly help me to find a solution.

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

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