[gmx-users] "Command Not Found"

[Natalie Stephenson]

Thanks loads ... that worked perfectly!! Environment configured!! :D
xxx

________________________________________
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 16:09
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] "Command Not Found"

Natalie Stephenson 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?
>

If you're having a problem with some external package, your best bet is to
contact those developers directly.  Your previous message said that you were
able to install the package and the executables were in /usr/local/gromacs/bin,
which probably just means your environment isn't configured properly:

http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation

If the installation was actually successful, this is all you should need to do,
as you would with any Gromacs installation, custom or otherwise.

-Justin

> 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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--
========================================

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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