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