[gmx-users] A problem with do_dssp command

[Justin Lemkul]

On 5/8/13 2:55 PM, zugunder wrote:
> Hi,
>
> Hi, I have a rather odd problem running do_dssp:
>
> $ do_dssp -h
> bash: do_dssp: command not found
>
> I am running GROMACS 4.5.7 under SL 6.3 and everything else seems to work
> fine.
>
> DSSP is also installed and should be OK:
>
> $ dssp -h
> DSSP 2.0.4 options:
>    -h [ --help ]         Display help message
>    -i [ --input ] arg    Input file
>    -o [ --output ] arg   Output file, use 'stdout' to output to screen
>    -v [ --verbose ]      Verbose output
>    --version             Print version
>    -d [ --debug ] arg    Debug level (for even more verbose output)
> ..........
>
> I am quite confused - is it possible that GROMACS package from EPEL (that I
> am using) lacks this program?
>

You can check this yourself by investigating the contents of the bin 
subdirectory of wherever Gromacs was installed.  You probably just need to make 
use of GMXRC to configure your environment.

http://www.gromacs.org/Documentation/Installation_Instructions#4.10._Getting_access_to_GROMACS_after_installation

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================