[gmx-users] minimization

[Justin A. Lemkul]

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
> 

-- 
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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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