Protein Structure & Molecular Modeling lab
Institute of Biosciences & Applications
NCSR "Demokritos", 15310 Ag. Paraskevi-Athens, Greece

 

Installation Instructions

GROMITA can be easily installed with the setup.pl installation perl script, which checks if all prerequisites are available and installs gromita.

   1. Install GROMACS and the programs it depends on
   2. Install Perl (in most Linux distributions it should be already installed)
   3. Install Perl/Tk using the CPAN module
            Make sure that the CPAN module is installed:
           $>perl -e 'use CPAN;'
            If it is installed no error message should appear.
            Switch user to root in order to make available perl/tk for all users and invoke a CPAN shell:
                 $>su
                 (type Password)
                 $>perl -MCPAN -e shell
            (if you are using Ubuntu type instead: $>sudo perl -MCPAN -e shell and type your user password, not the root)
            Install Perl/Tk:
                 $>cpan>install Perl/Tk
            some installation and testing messages will follow, and when complete type quit to exit the CPAN shell
   4. Extract the compresed file (e.g in your desktop)
   5. Open a terminal and cd to newly created directory
   The following steps must be done as root (superuser) for gromita to be available to all users:
      $>su
      (type Password:)

    6. Then type:
      $>perl setup.pl
   (If you are using Ubuntu, type instead: $>sudo perl setup.pl and when prompted enter your password (not the root))


      The setup script will then check for the installed perl version, its modules, gromacs path e.t.c. Note that Gromita may complain about some  version numbers, because it asks for the versions under wich it was developed. It will probably work well with much lower versions, just it has not been tested with them

     ------------------
      checking perl version...ok
      checking for required perl modules:
      File::HomeDir:  ok
      File::Spec:     ok
      Time::HiRes:    ok
      Carp:   ok
      Tk:     ok
      searching for GROMACS...ok
      counting processors...1
      searching for GROMACS dependences...FFTW: ok

      SETUP SUMMARY
      -----------
      Nothing missing

      Proceed with gromita installation? [y/n]



   7. When the checking for installed programs is finished the installation script will ask for verification before proceeding.

      Proceed with gromita installation? [y/n] y
      Starting installation
      Installation completed!
   9. Gromita is ready! Just type gromita and it will load
                                 

Gromita can be easily installed with the setup.pl installation perl script, which checks if all prerequisites are available and installs gromita.

  1. Install GROMACS and the programs it depends on
  2. Install Perl (in most Linux distributions it should be already installed)
  3. Install Perl/Tk using the CPAN module
      Make sure that the CPAN module is installed
      $>perl -e 'use CPAN;'
      if it is installed no error message should appear.
      Switch user to root in order to make available perl/tk for all users and invoke a CPAN shell
      $>su
      Password:
      #>perl -MCPAN -e shell
      (if you are using Ubuntu type instead: $>sudo perl -MCPAN -e shell and type your user password, not the root)
      install Perl/Tk:
      $>cpan>install Perl/Tk
      some installation and testing messages will follow, and when complete type quit to exit the CPAN shell
  4. Extract the compresed file (e.g in your desktop)
  5. Open a terminal and cd to newly created directory
  6. In order to have gromita available for all users and have the mspc option working you must install gromita as root
    7. $>su
    Password:
    #>perl setup.pl
    Note: If you are using Ubuntu, instead of the above type $>sudo perl setup.pl and when prompted enter your password (not the root)
  7. run the setup script:
    8. The setup script will check for the installed perl version, its modules, gromacs path e.t.c. Follow the instructions. Note that Gromita may complain about some version numbers, because it asks for the versions under wich it was developed. It will probably work well with much lower versions, just it has not been tested with them.
    $>perl setup.pl
    checking perl version...ok
    checking for required perl modules:
    File::HomeDir:  ok
    File::Spec:     ok
    Time::HiRes:    ok
    Carp:   ok
    Tk:     ok
    searching for GROMACS...ok
    counting processors...1
    searching for GROMACS dependences...FFTW: ok

    SETUP SUMMARY
    -----------
    Nothing missing
    Proceed with gromita installation? [y/n] 

  8. When checking for installed programs is finished the installation script will ask for verification before proceeding. Note that the following steps must be done as root (superman) for gromita to be available to all users:
    9. Proceed with gromita installation? [y/n] y
    Starting installation
    Installation completed!
  9. Gromita is ready! Just type gromita and it will load
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