[gmx-users] New DSSP vs do_dssp (gromacs-4.5.4)

Ahmad Randy run_d47 at yahoo.com
Thu Oct 13 11:16:19 CEST 2011

Hi All,

I understand that there were already some discussions about new DSSP exec with do_dssp in gromacs-4.5.4. I just want to make clear, is it true that this two DSSP and do_dssp do not compatible each other? 

I was running in Ubuntu 10.04, and this is what I got:

            do_dssp -f 300K.trr -s 300K.tpr -o dssp

I choose 5 'Mainchain'

            Fatal error:
            Failed to execute command: /home/madndy/dssp/dssp -na ddkbeHeQ ddvDjL4J > /dev/null 2> /dev/null

I already set the "export DSSP=/home/madndy/dssp/dssp", and also try the latest do_dssp.c (from gromacs-4.6) file for instalation. Still didn't work.

Are there are any suggestion or correction in my step? Or what version of gromacs that work well with DSSP? Or should I get the older version of DSSP that work with do_dssp? And where can I find the older version of DSSP because I can't find the older version in: http://swift.cmbi.ru.nl/gv/dssp/ . 

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