mustafa bilsel wrote:
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
This is still wrong. As I quoted in the previous message, the DSSP environment
variable has to point to the actual executable, *not* simply the directory that
contains it. Therefore:
export DSSP=/home/m/DSSP/dssp
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?
Probably due to incorrect environment variable settings.
-Justin
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
--
========================================
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
========================================
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