[gmx-users] minimization

[mustafa bilsel]

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
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