[gmx-users] gromacs synaptic package manager
Justin A. Lemkul
jalemkul at vt.edu
Sat Oct 2 14:56:54 CEST 2010
ahmet yıldırım wrote:
> I can not pass to pdb2gmx. (can you look at the attached photo).
>
I think you need to spend some time understanding how Linux/Unix commands work.
You're attempting to "cd pdb2gmx," and you're being told very clearly that
pdb2gmx is not a directory. It's an executable, you can't cd into it.
Per the instructions I sent before, you need to either add the location of your
Gromacs installation to your PATH (in whatever shell configuration file, likely
.bashrc) or source GMXRC every time you log in to a new terminal. Once your
Gromacs installation is recognized by your shell environment you can run all the
commands.
-Justin
> 02 Ekim 2010 15:22 tarihinde Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> yazdı:
>
>
> http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions#Getting_access_to_GROMACS_after_installation
>
> -Justin
>
> ahmet yıldırım wrote:
>
> Hi,
>
> When I run the pdb2gmx, it is giving the error as folllowing.
> What can I do?
>
> Thanks in advance
>
> ab at ab-desktop:~/Masaüstü/gromacs-4.5.1/src/kernel$ pdb2gmx -h
> The program 'pdb2gmx' is currently not installed. You can
> install it by typing:
> sudo apt-get install gromacs
> bash: pdb2gmx: command not found
> -h
> The program 'pdb2gmx' is currently not installed. You can
> install it by typing:
> sudo apt-get install gromacs
> bash: pdb2gmx: command not found
>
>
> 02 Ekim 2010 02:08 tarihinde Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>>> yazdı:
>
>
>
>
> ahmet yıldırım wrote:
>
> Dear Roland,
>
> Eventually I installed the installation steps with
> "./configure
> --prefix=$HOME/usr "as you said. can you send me the
> input file
> for test?
> I want to run a simulation. how can I do this?
>
>
> Please do some tutorial material. I sent you the link before.
>
> -Justin
>
> Thanks for your helps
>
>
> 2010/10/2 Roland Schulz <roland at utk.edu
> <mailto:roland at utk.edu> <mailto:roland at utk.edu
> <mailto:roland at utk.edu>>
> <mailto:roland at utk.edu <mailto:roland at utk.edu>
> <mailto:roland at utk.edu <mailto:roland at utk.edu>>>>
>
>
>
> Hi,
>
> either install as root by running:
> sudo make install
>
> or rerun the installation steps with ./configure
> --prefix=$HOME/usr
> to install it in your home directory.
>
> Roland
>
> 2010/10/1 ahmet yıldırım <ahmedo047 at gmail.com
> <mailto:ahmedo047 at gmail.com>
> <mailto:ahmedo047 at gmail.com <mailto:ahmedo047 at gmail.com>>
> <mailto:ahmedo047 at gmail.com
> <mailto:ahmedo047 at gmail.com> <mailto:ahmedo047 at gmail.com
> <mailto:ahmedo047 at gmail.com>>>>
>
>
>
> Dear justin,
>
> Thanks for your reply. I did that you said. I tried to
> install
> Gromacs 4.5.1but I failed it. I enter this line "
> ab at ab-desktop:~/Masaüstü/gromacs-4.5.1 make
> install " in
> terminal. What can I do? I am sorry. I am a new user.
>
> Thanks in advance
>
> 1. I installed fftw 3.2.2
> ab at ab-desktop:~/Masaüstü/ cd fftw-3.2.2
> ab at ab-desktop:~/Masaüstü/fftw-3.2.2
> ab at ab-desktop:~/Masaüstü/fftw-3.2.2 ./configure
> --enable-threads --enable-float
> ab at ab-desktop:~/Masaüstü/fftw-3.2.2 make
> ab at ab-desktop:~/Masaüstü/fftw-3.2.2 make install
>
> 2. I tried to install Gromacs 4.5.1
> ab at ab-desktop:~/Masaüstü/ cd gromacs-4.5.1
> ab at ab-desktop:~/Masaüstü/gromacs-4.5.1
> ab at ab-desktop:~/Masaüstü/gromacs-4.5.1 ./configure
> ab at ab-desktop:~/Masaüstü/gromacs-4.5.1 make
> ab at ab-desktop:~/Masaüstü/gromacs-4.5.1 make install
> Making install in include
> make[1]: Entering directory
> `/home/ab/Masaüstü/gromacs-4.5.1/include'
> Making install in .
> make[2]: Entering directory
> `/home/ab/Masaüstü/gromacs-4.5.1/include'
> make[3]: Entering directory
> `/home/ab/Masaüstü/gromacs-4.5.1/include'
> make[3]: Nothing to be done for `install-exec-am'.
> test -z "/usr/local/gromacs/include/gromacs" ||
> /bin/mkdir -p
> "/usr/local/gromacs/include/gromacs"
> /bin/mkdir: cannot create directory
> `/usr/local/gromacs':
> Permission denied
> make[3]: *** [install-pkgincludeHEADERS] Error 1
> make[3]: Leaving directory
> `/home/ab/Masaüstü/gromacs-4.5.1/include'
> make[2]: *** [install-am] Error 2
> make[2]: Leaving directory
> `/home/ab/Masaüstü/gromacs-4.5.1/include'
> make[1]: *** [install-recursive] Error 1
> make[1]: Leaving directory
> `/home/ab/Masaüstü/gromacs-4.5.1/include'
> make: *** [install-recursive] Error 1
>
>
>
> 2010/10/1 Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>>
>
>
>
>
>
> ahmet yıldırım wrote:
>
> Hi,
>
> I've installed GROMACS 4.0.3 and MPI
> libraries using
> Ubuntu 9.04 Synaptic Package Manager. What
> else
> should I do?
> I want to run a simulation in parallel on a
> single PC.
> Which commands should I enter the terminal?
>
>
> If I were you, I would uninstall this version
> (which is
> outdated by nearly 2 years!) and get version
> 4.5.1.
> Installing from source is quite easy. Not
> only will you
> benefit from hundreds of bug fixes and
> enhancements, but
> running in parallel on a multi-core machine is
> no longer
> MPI-dependent, making it somewhat easier.
>
> For usage and instructions, see the manual and
> any of the
> numerous tutorials linked here:
>
>
> http://www.gromacs.org/Documentation/Tutorials#General
>
> -Justin
>
>
> Thanks a lot for any instruction.
>
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu>
> <http://vt.edu> <http://vt.edu> |
>
> (540) 231-9080
>
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> -- gmx-users mailing list
> gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>>
>
>
> 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
> gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>>.
>
> Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> -- Ahmet YILDIRIM
>
> --
>
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>>
>
>
> 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
> gmx-users-request at gromacs.org <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>>.
>
> Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> -- ORNL/UT Center for Molecular Biophysics
> cmb.ornl.gov <http://cmb.ornl.gov>
> <http://cmb.ornl.gov>
> <http://cmb.ornl.gov>
>
> 865-241-1537, ORNL PO BOX 2008 MS6309
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>>
>
>
> 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
> gmx-users-request at gromacs.org <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>>.
>
> Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> -- Ahmet YILDIRIM
>
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
> 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> -- gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> 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 gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> --
> Ahmet YILDIRIM
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> 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 gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> --
> Ahmet YILDIRIM
>
> ------------------------------------------------------------------------
>
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list