[gmx-users] do_dssp segmental fault

archana sonawani ask.archana at gmail.com
Thu Aug 30 09:50:51 CEST 2012

Hi Deb,

I recently installed dssp for Gromacs 4.5.4 on RHEL4

You have to just copy the dsspcmbi downloaded from linux distribution to
/usr/local/bin (No need to set an environment variable DSSP if dspcmbi is
in /usr/loca/bin as it is the default path for gromacs)

Rename the dsspcmbi to dssp

chmod +x dssp is required  if doesn't show as executable. Run do_dssp at
any other location. This worked for me.


On Mon, Aug 20, 2012 at 10:49 AM, Debajyoti Ghosh <ghosh.dg at gmail.com>wrote:

> Dear gmx users,
> I recently upgraded the operating system to Ubuntu 12 and re-installed
> Gromacs 4.5.5. But I could not re-install dssp.
> I did the following:
> (1) I downloaded dsspcmbi from http://swift.cmbi.ru.nl/gv/dssp/
> Went to distributions- DSSPold - Linux Distributions to download
> dsspcmbi. (2) Moved to /usr/local/bin
> (3) sudo chmod +x dsspcmbi
> - do_dssp did not work.
> Then I (a) renamed dsspcmbi to dssp (b) ln -s dsspcmbi dssp
> - do_dssp still did not work.
> Then I did : export DSSP=/usr/local/bin/dssp
> - do_dssp still did not work as well.
> Please advise.
> Deb.
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Archana Sonawani-Jagtap
Junior Research Fellow,
Biomedical Informatics Centre,
Mumbai, India.

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