Thanks. I was mislead by the syntax in the online reference and forgot to change everything into bash scripting. You have been very very helpful!
2012/2/17 Justin A. Lemkul <jalem...@vt.edu>: > > > francesca vitalini wrote: >> >> export DSSP /home/cocktail/vitalini/gromacs_special/bin/dssp >> > > You forgot an '=' sign in the variable assignment. > > export DSSP=/home/... > > -Justin > > >> 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 >> >> >> >> > > -- > ======================================== > > 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
