Babel

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Description

Program Babel serves to conversion between diferent formates of molecular structures. As input files is Babel available to recognize following formats:

  • Alchemy
  • AMBER PREP
  • Ball and Stick
  • Biosym .CAR
  • Boogie
  • Cacao Cartesian
  • Cambridge CADPAC*
  • CHARMm*
  • Chem3D Cartesian 1
  • Chem3D Cartesian 2
  • CSD CSSR
  • CSD FDAT*
  • CSD GSTAT
  • Free Form Fractional
  • GAMESS Output*
  • Gaussian Z-Matrix
  • Gaussian Output*
  • Hyperchem HIN*
  • Mac Molecule
  • Macromodel
  • Micro World
  • MM2 Input
  • MM2 Ouput
  • MM3*
  • MMADS*
  • MDL MOLfile*
  • MOLIN*
  • Mopac Cartesian
  • Mopac Internal
  • Mopac Output
  • PDB
  • ShelX
  • Sybyl Mol*
  • Sybyl Mol2*
  • XYZ

As an output file can Babel write:

  • Alchemy
  • Ball and Stick
  • Cacao Cartesian
  • CAChe MolStruct*
  • Chem3D Cartesian 1
  • Chem3D Cartesian 2
  • ChemDraw Conn. Table*
  • CSD CSSR*
  • Gamess Input*
  • Gaussian Cartesian*
  • Gaussian Z-matrix
  • Hyperchem HIN*
  • IDATM
  • Mac Molecule
  • Macromodel
  • Micro World
  • MM2 Input*
  • MM2 Ouput
  • MM3*
  • MMADS*
  • MDL Molfile*
  • Mopac Cartesian
  • Mopac Internal
  • PDB
  • Report
  • Sybyl Mol*
  • Sybyl Mol2*
  • XYZ

Babel is capable of assigning hybridization, bond order, and connectivity when these elements are not present in the input file.

Use

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of babel and load default version of babel as

module avail babel/ # list available modules
module load babel   # load (default) module


If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail babel

and choose explicit version you want to use.

Documentation

On-line documentation is available.

Homepage

URL: http://server.ccl.net/cca/software/UNIX/babel/README.BABEL.shtml