Dear Justin, I have added your last reply to the end of this message. my shell type is bash. my dssp exe file is in /home/m/DSSP/dssp I wrote export DSSP=//home/m/DSSP/ as in gromacs web page, then I did do_dssp I have the below error. Although the dssp exe is in /usr/local/bin and also I did export, computer couldn't find dssp exe file.
What is the problem? What should I do? Best wishes Mustafa ----------------------------------------------------------------------------- Select a group: 5 Selected 5: 'MainChain' There are 90 residues in your selected group Reading frame 0 time 0.000 Back Off! I just backed up ddt2Vei2 to ./#ddt2Vei2.1# ------------------------------------------------------- Program do_dssp, VERSION 4.5.1 Source code file: do_dssp.c, line: 521 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddt2Vei2 ddPcoaqM > /dev/null 2> /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- mustafa bilsel wrote: > Hi, > I have a problem with dssp programme. > I have the programme in /home/m/DSSP. When I write > export DSSP=/usr/local/bin > and then I check /usr/local/bin I couldn't see dssp. > How can I handle this problem. I have caheceked gromacs website > > export DSSP=/path/to/dssp > > setenv DSSP /path/to/dssp > > commands are written. > Could you write export DSSP=/path/to/dssp command according to me. > The proper setting for the environment variable is explained in great detail here: http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note the line "If this is not the case, you must set the DSSP environment variable accordingly, pointing to the actual dssp executable, not just the PATH to it." > And also I use Ubuntu 10.04, setenv is not used, if I try to install it, I > see the package not found message. > What should I do about it? > Learn what your shell uses and apply it. You're more than likely running bash, in which case "export" is the command to use. -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