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. Thanks again
2012/2/17 Justin A. Lemkul <[email protected]>: > > > 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 [email protected] > 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 [email protected]. > 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 [email protected] [email protected] +49 3083875776 +49 3083875412 -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
