MOLDEN a visualization program of molecular and electronic structure
MOLDEN a pre- and post processing program of molecular and electronic structure
Molden is a package for displaying Molecular Density from
the Ab Initio packages GAMESS-UK , GAMESS-US
and the Semi-Empirical packages Mopac/Ampac, it also supports
a number of other programs via the Molden Format.
Molden reads all the required information from the
GAMESS / GAUSSIAN outputfile.
Molden is capable of displaying Molecular Orbitals,
the electron density and the Molecular minus Atomic density.
Either the spherically averaged atomic density or the oriented ground state
atomic density can be subtracted for a number of standard basis sets.
Molden supports contour plots, 3-d grid plots with hidden
lines and a combination of both.
It can write a variety of graphics instructions;
postscript, XWindows, VRML, povray, OpenGL, tekronix4014, hpgl, hp2392 and Figure.
Both Xwindows and OpenGL
versions of Molden are also capable of importing
and displaying of chemx, PDB, and a variety of mopac/ampac files and lots
of other formats.
Molden also can animate reaction paths and molecular vibrations. It can calculate
and display the true or Multipole Derived Electrostatic Potential
and atomic charges can be fitted to the Electrostatic Potential calculated
on a Connolly surface.
Molden also features an stand alone forcefield program ambfor, which can
optimise geometries with the combined Amber (protein) and GAFF (small molecules)
force fields. Atom typing can be done automatically and interactively from
within Molden, as well as firing optimisation jobs.
Molden has a powerful Z-matrix editor which give full control over the geometry
and allows you to build molecules from scratch, including polypeptides.
Molden was also submitted to the
QCPE (dead?) (QCPE619), allthough
Xwindows version is considerably running behind on the current one.
Molden5.7 Adds editable text fields that are longer than the visible string and introduces a new way of selecting a range of amino acids.
Molden5.6 introduces interfaces to the open source packages openbabel and pharmer.
Openbabel is used to create 2D images of the molecules in a .sdf file.
It is also used to do 2D fingerprint searching.
Pharmer is used to pharmacophore (3D) searching against indexed databases of .sdf files.
Molden5.4 Missing hydrogens atoms of HETATM molecules (pdb files) are stored locally. Pdb files can now be clipped. This version ONLY adds or rescues protein functionality with respect to version 5.3. If you are not interested in proteins you can skip this version.
Molden5.3 Fixes missing residues. Introduces an alternative way of generating rotamers, without using z-matrices. This potentially a faster algorithm.
Molden5.2.1 Supports Movie making through avconv/ffmpeg.
Molden5.2 calculates the Electron Localization Function (ELF).
molden5.1: Updated code of ambfor/ambmd to speed up optimisations/MD ofproteins solvated in water (Jan, 2014).
molden5.0.6: Add hydrogen to HETATM residues of PDB files works again with this version.
Introducing a native windows executable of gmolden here (Apr, 2013)
molden5.0.5: Molden can now localize orbitals via the Boys scheme
molden5.0: Introduces a crystal optimiser with the Gaff forcefield(Dec 10, 2010)
molden4.8: Problem with reading G09 z-matrix output fixed (Feb 1, 2010)
molden4.8: addition of hydrogens to hetatm records of pdb entries
molden4.8: optimisation of hydrogen bonds, waters and histidine residues
molden4.8: retrieving pdb files from the internet in the file selector
molden4.8: Support for calculated NMR spectrum in combination with Gaussian outputs
molden4.8: simple MD program, ambmd
ambfor: important update to ambfor force field module
molden4.7: partial optimisations are now possible (click here)
molden4.7: molden can now hold multiple structures in memory
molden4.6: features a forcefield optimisation program Ambfor (AMBER/GAFF forcefields)
molden4.6: now better supports Gaussian IRC optimisations and MP2 optimisations
molden4.6: Support for Orca.
molden4.6: Support for G functions with Gaussian.
molden4.6: features dynamic memory allocation for proteins and display of dipole moment.
full interactive opengl version of molden: gmolden
Register as a Molden User
How to get a copy of Molden ?
What are the latest changes/bugfixes to Molden ?
The Z-Matrix Editor
Using Molden with Gaussian outputs
Using Molden with Mopac
Using Molden with programs OTHER than Gamess/Gaussian/Mopac
How to set up MOLDEN to use helper programs
Molden command line flags
Currently tested platforms
Controlling Molden by keywords
Viewing Electron Density plots with Molden
Exceeding MaxNum of Orbitals!
Viewing/Editing Protein Structure with Molden
Optimization of small molecules with the AMBFOR module
Optimization of docked small molecule protein complex with the AMBFOR module
Viewing Reaction Paths with Molden
Viewing Vibrations with Molden
Calculation of ESP fit charges with Molden
GMOLDEN OpenGL Gallery
Creating an isodensity surface
colorcoded with the electrostatic potential.
Using Molden as a viewer for chemical mime types
How to View/Create animations with Molden
MOLDEN VRML orbital/electron density service
MOLDEN VRML Gallery
The Laplacian of the Electron Density
How we can build a crystalline structure with Molden?
OpenGL via an external helper program (superseded by gmolden)
Mail comments/complaints to author