[gmx-users] "Command Not Found"

[Tsjerk Wassenaar]

Hi Natalie,

You're in the wrong place, and probably trying the wrong thing. The
FDAtools are not part of Gromacs and if you encounter issues with them
you should raise it with the authors. They may have a user list too.

Aside from that, the FDAtools seem to be an R package. That means that
they will offer you extended functionality within R, and not as
command line tools.

Cheers,

Tsjerk



On Mon, May 16, 2011 at 5:01 PM, Natalie Stephenson
<Natalie.Stephenson at postgrad.manchester.ac.uk> wrote:
> 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?
>
> Thanks
> Natalie
>
> ________________________________________
> 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?
>
> -Justin
>
>> 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
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands