I have download dsspcmbi.zip and extract the dssp folder into /cygdrive/c/cygwin/usr/local/bin/ directory. Then set the environment variable export DSSP=/cygdrive/c/cygwin/usr/local/bin/dssp for bash. then I have gone to my folder by using cd where all my md files were present i.e. /cygdrive/c/gromacs-4.0.7. At last I executed the command do_dssp -f traj.xtc -s md.tpr -n index.ndx -aa area.xvg after preformed this I still got an error i.e. Fatal error: failed to execute command: /cygdrive/c/cygwin/usr/local/bin/dssp ddrN1s8q dd4bcjqa > /dev/null 2> /dev/null
Please rectify this.. -- Pawan
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