[gmx-users] dssp problem

[Justin A. Lemkul]

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:

http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp

-Justin

> 
> -- 
> Pawan
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================