[gmx-users] Question about installing DSSP on Ubuntu 12.10

Justin Lemkul jalemkul at vt.edu
Tue Oct 8 14:01:50 CEST 2013

On 10/8/13 7:28 AM, Mass wrote:
>   I am trying to install "DSSP" in Ubuntu 12.10, I just download it from Ubuntu software centre but when I run it I am getting the following error, any solution? I have checked all the mail list archive and could not solve my problem
> Fatal error:
> Failed to execute command: /usr/local/bin/dssp -na ddZGP3ET ddjex0J9 > /dev/null 2> /dev/null

You probably need to set -ver appropriately in your do_dssp command.

> I google it and found this on ubuntu forum but I followed it and still I am getting error
> up vote
> 0
> down vote
> accept DSSP is not in official ubuntu repositories, but you can install it manually:
> sudo wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 -O /usr/local/bin/dssp
> or
> sudo wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-i386 -O /usr/local/bin/dssp
> And for the end:
> sudo chmod a+x /usr/local/bin/dssp
>    I have done this but still I am getting Fatal error: DSSP executable (/opt/dssp/bin/dssp) does not exist (use setenv DSSP) –

If you have set the $DSSP environment variable to point to /opt/dssp/bin/dssp, 
then you should get a fatal error, because based on the above commands, your 
dssp is in /usr/local/bin/dssp, which is the default location where do_dssp 
looks for it.  If $DSSP is set, it overrides the default, which in your case is 
causing problems.

>   Also appreciate if any one can give simple and step-by step instruction to insall dssp-2.2.1 from website. I mean after downloading dssp-2.2.1.tgz and extracting it what should I do? –

Unzip the archive, compile from source if you are downloading source (ignore if 
you are downloading a binary), move the binary wherever you want it, set $DSSP 
only if you are not putting it in /usr/local/bin.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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