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MOLEKEL

MOLEKEL ist ein 3D-Molekülgrafikprogramm mit vielfältigen Möglichkeiten zur Darstellung der Struktur und Eigenschaften (Orbitale, Elektronendichte usw.) von Molekülen. Es erlaubt u.a. die Überlagerung von Strukturen. MOLEKEL kann die Ausgabedateien von Gaussian, GAMESS und vielen anderen Programmen sowie pdb-Files und reine cartesische Koordinaten lesen.

General

Description

 MOLEKEL is an interactive, three-dimensional molecular graphics package:
            -  represents molecules as wire frame, stick, ball-and-stick and spacefill representations.
            -  measures atom-atom distances, angles and torsion angles.
              - an superimpose molecules.
            - calculates and displays isosurfaces of electron and spin densities as well as molecular orbitals from the output of various electronic structure calculation programs.
            - uses texture mapping to color code any surface according to e.g. the molecular electrostatic potential.
            -  is able to clip any surface by a clipping plane and to render it transparent.
            - can animate and display vibrational modes.
            - can animate geometry optimizations and multiple coordinate PDB and XYZ files.
            - can display the dipole moment of a molecule
            - can export coordinates in PDB and XYZ format in original or modified orientation.
            - can save pictures in RGB, TIFF and JPEG format.
            - can render pictures at any size, i.e. larger than screen size.
            - can automatically generate series of pictures of animations (frequencies, series of coordinates).
      · Supported output file formats of electronic structure calculation programs:· GAUSSIAN,  GAMESS US,  ADF,  ZINDO, MOS, HONDO, PRDDO, NBO orbital coefficients together with a Gaussian logfile, MOLDEN file format   
      · Supported coordinate formats:· PDB,  XYZ,  free format
      · Supported grid formats: GAUSSIAN CUBE files, ADF TAPE41 files, MACU (MOLEKEL's format)

Versions

Hardware

Version

Linux Cluster X86_64

5.4.0

Setup and Access for Molekel at LRZ

The modules package controls access to software.

To use the default version of Molekel, include the line:

 % module load molekel

Running MOLEKEL

Molekel can be run interactively using the command:

% Molekel

and MOLEKEL should start, displaying the following "molekel main window" and the "main interface":

 

molekel1

 

Manuals

A manual in HTML, PDF or PostScript format can be found at the MOLEKEL website.
Pressing the "help" button in the main interface will also make the manual available in a web browser.

Support

If you have any questions or problems with MOLEKEL installed on LRZ platforms please contact Dr. Momme Allalen, phone: (089) 35831-8816, preferably by Email: allalen (at) lrz-muenchen.de.