export DSSP /home/cocktail/vitalini/gromacs_special/bin/dssp 2012/2/17 Justin A. Lemkul <jalem...@vt.edu>: > > > francesca vitalini wrote: >> >> Thanks! >> However now I jet another error >> -bash: export: `/home/cocktail/vitalini/gromacs_special/bin/dssp': not >> a valid identifier >> even though the path is correct and I have saved the binary file that >> I downloaded with the name dssp. Do you kno if after downloading I >> have to do anything with the binary file to make it work? n the dssp >> website they don't write anything about it. > > > What was your exact export command? > > -Justin > > >> Thanks again >> >> >> >> 2012/2/17 Justin A. Lemkul <jalem...@vt.edu>: >>> >>> >>> francesca vitalini wrote: >>>> >>>> Dear all, >>>> In order to get the secondary structure of my pdb file I need to run >>>> the do_dssp program. When I try to run it however I get the following >>>> error >>>> >>>> Program do_dssp, VERSION 3.3.1 >>>> Source code file: do_dssp.c, line: 448 >>>> >>>> Fatal error: >>>> DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) >>>> >>>> So I went to the http://swift.cmbi.ru.nl/gv/dssp/DSSP_5.html website >>>> and downloaded the program. when then I try to settle the environment >>>> variable >>>> >>>> set an environment variable DSSP pointing to the dssp executable, e.g.: >>>> >>>> setenv DSSP /opt/dssp/bin/dssp >>>> >>>> then I get the following error message: >>>> >>>> -bash: setenv: command not found >>>> >>> You need to use "export" for bash; "setenv" is for csh. >>> >>> export DSSP=/opt/dssp/bin/dssp >>> >>> -Justin >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface >>> or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- Francesca Vitalini PhD student at Computational Molecular Biology Group, Department of Mathematics and Informatics, FU-Berlin Arnimallee 6 14195 Berlin vital...@zedat.fu-berlin.de francesca.vital...@fu-berlin.de +49 3083875776 +49 3083875412 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
