[gmx-users] Installing DSSP

Erik Marklund erik.marklund at kemi.uu.se
Fri Feb 3 16:38:04 CET 2017

Dear Soumadwip,

This is not a problem with do_dssp, but with your deep installation. My guess is that you have not completed the installation of dssp.

Kind regards,
Erik Marklund, PhD
Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>

On 3 Feb 2017, at 07:51, soumadwip ghosh <soumadwipghosh at gmail.com<mailto:soumadwipghosh at gmail.com>> wrote:

Hello all,

I am trying to install dssp in centos 7 for determining the secondary
structure of a protein in combination with do_dssp. These are the steps I

1. installation directory : /opt/apps/dssp/dssp-2.2.1/

2. but there is no dssp executable in the dssp-2.2.1 directory

3. however there was a dssp.o file in the obj directory of dssp-2.2.1

4. we renamed the dssp.o file to dssp and moved it to dssp-2.2.1 directory

5. ln -s /opt/apps/dssp/dssp2.2.1/dssp /usr/local/bin/

6. export dssp=/usr/local/bin/dssp

but inspite of executing the above steps, when we run the do_dssp command we get
the following error : Fatal error: DSSP executable
(usr/local/bin/dssp/dssp) does
not exist (use setenv DSSP)

PS. we are using bash

I have read various threads on the errors related to do_dssp but could
not find a solution.

Any kind of help would be appreciated.


Soumadwip Ghosh

Research Associate

Indian Institute of Technology Bombay

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