[gmx-users] dssp problem

Justin A. Lemkul jalemkul at vt.edu
Sat May 1 17:23:44 CEST 2010

pawan raghav wrote:
> 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..

Your environment variable is wrong.  If you placed a "dssp" folder in 
/usr/local/bin, then the actual executable is located in 
/usr/local/bin/dssp/dssp.  Have a look at the usage notes:



> -- 
> Pawan


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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