[gmx-users] getting dssp executable

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 17 15:13:20 CET 2012

francesca vitalini wrote:
> Dear all,
> In order to get the secondary structure of my pdb file I need to run
> the do_dssp program. When I try to run it however I get the following
> error
> Program do_dssp, VERSION 3.3.1
> Source code file: do_dssp.c, line: 448
> Fatal error:
> DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)
> So I went to the http://swift.cmbi.ru.nl/gv/dssp/DSSP_5.html website
> and downloaded the program. when then I try to settle the environment
> variable
> set an environment variable DSSP pointing to the dssp executable, e.g.:
> setenv DSSP /opt/dssp/bin/dssp
> then I get the following error message:
> -bash: setenv: command not found

You need to use "export" for bash; "setenv" is for csh.

export DSSP=/opt/dssp/bin/dssp



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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