[gmx-users] Problem running do_dssp

Dipankar Roy DRoy at brooklyn.cuny.edu
Mon Aug 12 22:29:55 CEST 2013

I am trying to use do_dssp to generate a secondary structure map over time for a 10-ns simulation. I have installed dssp_2.2.0 at the usual /usr/local/bin
I tried running it with the following command line
do_dssp -f md.xtc -s md.tpr -o ss.xpm -sc ss.xvg -dt 100 -tu ps; but ended up with the following error.

Thanks in advance for your help.

Selected 4: 'Backbone'
There are 424 residues in your selected group
dssp cmd='/usr/local/bin/dssp -i dd5Yvoh4 -o ddazDUUO > /dev/null 2> /dev/null'
Reading frame       0 time    0.000   
Back Off! I just backed up dd5Yvoh4 to ./#dd5Yvoh4.1#

Program do_dssp, VERSION 4.6.3
Source code file: /home/rsd/gromacs-4.6.3/src/tools/gmx_do_dssp.c, line: 669

Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver option.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

"God is a DJ" (Faithless)


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