[gmx-users] "Command Not Found"

Natalie Stephenson Natalie.Stephenson at postgrad.manchester.ac.uk
Mon May 16 17:01:51 CEST 2011

Sorry for the confusion - didn't mean I'd used a wildcard when typing the commands ... just meant I get that response for both commands.

They're an add on created from a the Molecular BioMechanics group (http://projects.eml.org/mbm/website/fda_gromacs.htm) - I've downloaded they're software as they mention:

Installing the FDAtools package:
FDAtools depends on bio3d and SparsM. Please download the bio3d package.
A a Mac / Linux user, check that your R_LIBS variable points to the folder in which packages should be installed (insert an export R_LIBS="..." in your .profile / .bashrc if not previously done).
Install bio3d by executing 'R CMD INSTALL bio3d_1.0-6.tar.gz'.
Install SparseM by executing 'install.packages("SparseM")' in an R console.
Now we are ready to install FDAtools, just type 'R CMD INSTALL FDAtools_0.9.tar.gz' on the command line.

And downloaded the 'gromacs_4.0.5_pf' that they have (FDA-Gromacs).  Is it likely to be some problem with the FDA-Gromacs package installation (the one I mentioned below) ... or is it likely to be something else? 


From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
Sent: 16 May 2011 15:56
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] "Command Not Found"

Natalie Stephenson wrote:
>  Hi All,
> Sorry to bug you all about this - it's been mentioned a few times but I
> can't find an answer that seems to relate to the situation I've got.
> I'm trying to use the g_fdaconv / g_fdatools within gromacs 4.0.5,
> however, everytime I type the commands I get 'g_fda*: command not found'.

Using wildcards will not find command names.

> These are present in the /usr/local/gromacs/bin directory - however when
> I've checked over the config.log they haven't installed.  I'm not sure I

OK, so you have an executable installed, but it didn't install?  Can you please
clarify?  Neither g_fdaconv or g_fdatools are standard Gromacs utilities - are
they some sort of external package or add-on?


> understand what's happened - the installation was done by downloading
> followed by ./configure, make, make install, and everything else seems
> to be functioning fine.  What is it I've missed?
> Can anyone shed any light on my (probably completely stupid) problem?!
> Thanks loads,
> Natalie
> ------------------------------------------------
> Natalie Stephenson, B.Sc
> PhD Research Associate
> Manchester Interdisciplinary Biocentre
> 131 Princess Street
> Manchester
> M1 7DN
> x65816
> ------------------------------------------------


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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