Re: [gmx-users] gromacs synaptic package manager

[Justin A. Lemkul]

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 <jalem...@vt.edu 
<mailto:jalem...@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

        a...@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 <jalem...@vt.edu
        <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
        <mailto:jalem...@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 <rol...@utk.edu
        <mailto:rol...@utk.edu> <mailto:rol...@utk.edu
        <mailto:rol...@utk.edu>>
               <mailto:rol...@utk.edu <mailto:rol...@utk.edu>
        <mailto:rol...@utk.edu <mailto:rol...@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 <ahmedo...@gmail.com
        <mailto:ahmedo...@gmail.com>
               <mailto:ahmedo...@gmail.com <mailto:ahmedo...@gmail.com>>
                  <mailto:ahmedo...@gmail.com
        <mailto:ahmedo...@gmail.com> <mailto:ahmedo...@gmail.com
        <mailto:ahmedo...@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 "
                      a...@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
                      a...@ab-desktop:~/Masaüstü/ cd fftw-3.2.2
                      a...@ab-desktop:~/Masaüstü/fftw-3.2.2
                      a...@ab-desktop:~/Masaüstü/fftw-3.2.2  ./configure
                      --enable-threads --enable-float
                      a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make
                      a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make install

                      2. I tried to install Gromacs 4.5.1
                      a...@ab-desktop:~/Masaüstü/ cd gromacs-4.5.1
                      a...@ab-desktop:~/Masaüstü/gromacs-4.5.1
                      a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 ./configure
                      a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make
                      a...@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 <jalem...@vt.edu
        <mailto:jalem...@vt.edu>
               <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
                      <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@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

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                      --         Ahmet YILDIRIM

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               --         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

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        -- 
        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

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--
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

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