TmoleX

TmoleX is an interactive graphical interface, molecule builder and QM job environment for Turbomole.

The current version is 17.
The home page is http://www.cosmologic.de/turbomole/tmolex.html.
The binary is in /temp4/bio//TURBO/TmoleX17/TmoleX/TmoleX
The documentation is in /temp4/bio/TURBO/TmoleX14/documentation/Tutorial-tmolex-4-0.pdf
There is a instruction video in http://www.cosmologic.de/turbomole/tmolex/online-video-tutorial.html.

To run it, you must simply write
TmoleX

On some systems, you might first set
export LIBGL_ALWAYS_SOFTWARE=1
otherwise, no molecule is show in the molecule builder.

The installation was simple:
chmod +x TmoleX40Linux64.bin
./TmoleX40Linux64.bin
and follow the instructions on the screen.

  1. Start TmoleX
    TmoleX
  2. Select New Project
  3. Select a directory
  4. Open 3D Molecular Builder
  5. Click on atoms
  6. Build the molecule
  7. Save it

To show vibrational frequencies

  1. TmoleX
  2. Select a NewProject
  3. Open job/Control file
  4. Select the proper file
  5. Click on the project on the left-hand tree
  6. Open 3D molecular builder
  7. Click on Vib. Modes
  8. Click on the desired mode
  9. Click on Play

Build molecules

  1. Open 3D Molecular Builder
  2. You can start from an existing molecule, from Smiles, from a 2D scetch of from fragments
  3. Click on the pencil (on the left) to build atom-wise.
  4. You can add H atoms, but only atom-wise: Select an atom; check that hybridization is properly set and then click on saturate. (You can select all atoms by Ctrl-A, but the defalut of hybridization, custom, does not allow H atoms to be added).

Visualisation

You can quite conveniently show MOs, electron density, electrostatic potential (e.g. mapped on the electron density (use 0.002 level).
Pictures can be exported as png images.
Background colour can be changed.


If you have problems of running Turbomole features within TmoleX (e.g. tidy up with UFF or viewing orbitals), this probably indicates that you are not allowed to run the Turbomole version in your path.
This is indicated by "TmoleX (client)" on your window.
To solve this (Uwe 28/5-15):
  1. Start TmoleX
  2. Open a new project
  3. Right-click on the project name in the left-most window
  4. Select open shell
  5. echo $TURBODIR
  6. $TURBODIR/scripts/sysname
  7. ls -l $TURBODIR/bin/`sysname`