[gmx-users] getting dssp executable

francesca vitalini francesca.vitalini11 at gmail.com
Fri Feb 17 14:54:19 CET 2012

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

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

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

Any help?

Francesca Vitalini

PhD student at Computational Molecular Biology Group,
Department of Mathematics and Informatics, FU-Berlin
Arnimallee 6 14195 Berlin

vitalini at zedat.fu-berlin.de
francesca.vitalini at fu-berlin.de

+49 3083875776
+49 3083875412

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