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: [email protected]
[[email protected]] on behalf of Justin A. Lemkul
[[email protected]] 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
======================================== -- gmx-users mailing list
[email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please
don't post (un)subscribe requests to the list. Use the www interface or send
it to [email protected]. Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
