[gmx-users] What much time does DSSP need to analyze lysozyme?

Mark Abraham Mark.Abraham at anu.edu.au
Sun Jun 28 16:37:40 CEST 2009

Chih-Ying Lin wrote:
> Hi
> 1. After compiling, the two following files are created.
> dsspcmbi
> dsspcmbi.exe
> 2. The path of the DSSP file is   /usr/local/bin/DSSP.
> Both dsspcmbi and dsspcmbi.exe  are in the file /usr/local/bin/DSSP.

"file" is a distinct concept from "directory".

> 3. So, the last step i type the command in my .profile.
> setenv dssp /usr/local/bin/DSSP
> export dssp= /usr/local/bin/DSSP
> export PATH=$PATH:$DSSP
> Is it correct ?

No. You are probably confusing C-shell and bash syntax, and need to be 
aware that variable names are case sensitive.

> 4. I also have Gromacs in my MAC.
> And I type the following command.
> do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc
> secondary-structure.xvg
> For running 5 minutes, the following files are created and DSSP still
> keep running.
> Is anything wrong here?

Probably. You need to follow the DSSP installation instructions more 

Please stop sending multiple emails with the same content. They won't 
help you get a response :-)


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