[gmx-users] do_dssp file format

David van der Spoel spoel at xray.bmc.uu.se
Mon Jan 14 18:57:21 CET 2008

ABEL Stephane 175950 wrote:
> Yes, Mark i have taken a look in your previous message
> To test my dssp program I took a pdb from the protein data bank: 1HRC. This pdb contains only one protein (and one frame). The DSSP program works fine with it and I obtain an output. So To test my do_dssp i also used this pdb. In this case when i choose MainChain 5 or other choices I obtain the same message described below and no output. I think, I have set correctly the DSSP environment variable because i have not the Fatal error:
> DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP). Moreover i think that ten minutes is not to short to process one config indeed the DSSP program take less than 2 seconds to compute the secondary structure of the protein in 1HRC pdb file.
> So i very frustrated...
> Stefane
so if you run

setenv DSSP `which dssp`
echo 1 | do_dssp -f 1HRC -s 1HRC

you get no output? do you have write permission in the work directory?

David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

More information about the gromacs.org_gmx-users mailing list