[gmx-users] do_dssp

Mark Abraham Mark.Abraham at anu.edu.au
Wed Apr 4 14:25:32 CEST 2012

On 4/04/2012 10:02 PM, Justin A. Lemkul wrote:
> Bernhard Knapp wrote:
>> Hi
>> I have some problems to get do_dssp running:
>> I downloaded the binary of dssp from http://swift.cmbi.ru.nl/gv/dssp/ 
>> . Then I extracted it using "gunzip dssp-2-linux-i386.gz". Next I 
>> copied it to the correct location: "cp dssp-2-linux-i386 
>> /usr/local/bin/dssp" and gave the user the right to execute the binary.
>> If I call dssp in an arbitrary directory (e.g.  "dssp -i test.pdb -o 
>> test.dssp") it works fine.  However, if I call it via do_dssp (e.g. 
>> "do_dssp -f test.xtc -s test.tpr -o test.xpm") I get the following 
>> error: "Fatal error: Failed to execute command: /usr/local/bin/dssp 
>> -na ddZ2pWoM ddjmIN4j > /dev/null 2> /dev/null". If I try to see what 
>> is going wrong via executing "/usr/local/bin/dssp -na ddZ2pWoM 
>> ddjmIN4j" directly in the shell then I get "unknown option -n".
>> Google did not help me since most people who got this error had dssp 
>> in the wrong path. In my case it definitly finds the executable but 
>> in the execution something goes wrong ...
>> What am I doing wrong?
> The problem is that the dssp syntax has changed and the Gromacs code 
> currently can't handle that syntax.  A patch has been proposed in the 
> development version but it has not yet been incorporated into the git 
> repository.  You could make the modifications to the source yourself 
> by following:
> https://gerrit.gromacs.org/#/c/687/

Or dig around on the dssp site to get the old version.


More information about the gromacs.org_gmx-users mailing list