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

Justin Lemkul jalemkul at vt.edu
Wed Oct 9 13:49:14 CEST 2013

On 10/9/13 6:42 AM, Mass wrote:
> Hi Justin
> Thanks for your answer but I could not solve the problem, sorry
> Can you tell me how can I fix this part? the highlighted part is your answer
>> 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 wgetftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64
> <ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64>-O
> /usr/local/bin/dssp
>> or
>> sudo wgetftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-i386
> <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.
> How can I resolve this?

If your dssp executable is /usr/local/bin/dssp, do not set the DSSP environment 
variable as that is the default location that do_dssp will look for.  If your 
dssp executable is somewhere else, set DSSP to indicate its location.



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


More information about the gromacs.org_gmx-users mailing list