gOpenMol is a tool for the visualization and analysis of molecular structures and their chemical properties. The program uses Tcl/Tk scripting engine and can thus be easily extended without modifying the kernel code. gOpenMol can also be extended by writing extensions using sharable objects (Linux/Unix) and dynamic data exchange (Windows) modules. Moreover there is a set of programs and utility functions included in gOpenMol.

gOpenMol can be used for the display and analysis of

• molecular structures and properties calculated with external programs,
• molecular dynamics trajectories,
• isocontour surfaces of grid data, such as molecular orbitals and electron densities.
• cut planes through grid data sets, and it can also be used to make short animations where a cut plane travels through a molecule grid data.

• The program can also be used together with electrostatic potentials from programs like GaussianXX, GAMESS Jaguar, UHBD (University of Houston Brownian Dynamics), AutoDock and the GRID programs.

Software

Several different input coordinate and binary traectory file formats can be imported, displayed and analyzed in gOpenMol. Isocontour surfaces and cross sections of grid data can also be displayed in gOpenMol. The program has a graphical user interface (GUI) and an internal command line interpreter based on the Tcl/Tk.

Further information about the Tcl/Tk language and library use can be found at: http://www.tcl.tk/.

Hardware

gOpenMol is implemented using either the SGI OpenGL or MESA (http://www.mesa3d.org/) graphics libraries. When using the MESA graphics library it is possible to turn gOpenMol into pure X-Windows application, where no extra graphics hardware is needed.

gOpenMol is currently supported on the following platforms. The primary development platforms Linux (Intel) and Windows are marked with [*]. Versions for the other platforms might be available at some time in the future.

• IBM AIX 5.2 PowerPC 
• PC/Linux  [*]
• SunOS 5.9 Sparc
• Windows 95/98/NT/2000/XP (WIN32) [*]

Anyone interested to support gOpenMol on a platform is welcome to join!

Supported file formats

gOpenMol supports the following molecule coordinate input formats...

• ADF output log file
• CHARMm/CHARMM
• Chemical Markup Language (CML^TM)
• Chem3D binari file
• DL_Poly CONFIG file
• A frame from a trajectory
• Gamess DAT, IRC and LOG output files
• Gaussian formatted checkpoint file
• GROMACS
• GROMOS
• HyperChem
• Insight (car files)
• Mol2
• Mopac
• Mumod
• OpenMol (center binary file)
• PDB (Brookhaven Protein Data Bank format)
• Spartan binary file
• Tinker coordinate file
• Turbomole grid file
• UHBD qcd coordinate file
• Xmol xyz coordinate file
• GXYZ general xyz coordinate file
• YASP

... binary trajectory formats...

• Amber
• Cerius2
• CHARMm/CHARMM
• Discover
• DL_Poly
• GROMACS
• Gromos (mind you, this is the old GROMOS format)
• HyperChem (This format has not yet been tested with the latest version.)
• MUMOD
• XPLOR
• YASP

... and ascii trajectory formats.

• DL_Poly trajectory format
• GROMOS96 trajectory format
• TINKER multi frame coordinate trajectory format
• XMOL xyz multi-step data sets. The included Xvibs program enables the display of vibrational modes from the GAUSSIANXX and GAMESS programs.

Extensive display of isocontour surfaces and cut planes for

• Orbitals, densities ... from GAUSSIANXX set of programs.
• Connolly type surfaces using the ProbeSurf program.

Utility programs

The utility programs are located in the directorybin/ and the source code is available in the directory utility/, except for the MolPro-program, which can be downloaded from the Internet. Some of the programs can be run through the menu Run in the GUI-window and the rest of the programs can be run in a DOS-terminal.

Programs that can be run through the menu Run in the GUI-window.

AutoDock2plt

Converts an AutoDock map file to a plt file.

ContMan

Contour (plt) files can be manipulated by adding or substracting two contours.

Gamess2plt

Converts a Gamess "cube" PUNCH file to a plt file.

gCube2plt/g94cub2plt

Converts a cube file from the GaussianXX program into a binary format known by gOpenMol.

Jaguar2plt

Converts a Jaguar plot file to a gOpenMol plt file.

Join Gamess IRC files

Joins frames from an IRC calculation to amn XMOL file.

Kont2plt

Converts a Grid data file to a formatted or an unformatted plt file.

Pltfile

This program can be used to format a binary plot file or to make a formatted file into binary. This program is helpful if you want to move the plot file from one computer hardware to another.

Probesurf (Connolly)

Generates a Connolly type of surface around the molecular system.

Socket server/client

Bits and pieces to send structures between two gOpenMol programs.

TMole2plt

Converts a TurboMole grid file to a plt file.

UHBD2plt

Converts a UHBD formatted and unformatted PHI grid files into the plt format used by the gOpenMol program.

Xvibs (conversion)

Program to generate a multi structure XMOL file for animation from a variety of quantum chemistry programs.

Programs that can be run in a DOS-window.

ambera2b

Converts a formatted ascii AMIER trajectory into an unformatted one. gOpenMol can handle only unformatted AMIER trajectories.

charmmtrj

This program makes the formatted/binary tranformation for a CHARMM dynamics trajectory file.

convert

Converts the output search results (FDAT) from Cambridge Structural Database into separate PDI files.

MolPro

Converts Molpro2002.1 cube file with one or more orbitals to gOpenMol2.1 binary plt file and one crd file. At the moment, gradients or laplacians are not supported. The utility program can be dowloaded from Lauri Lehtovaara's we page at http://www.cc.jyu.fi/~lauri/progs.html.

sybyl2amber

Converts a formatted ascii Sybyl trajectory into an unformatted AMBER one.

trajmerge

Merges two CHARMM trajectory files into one.

xplor2charmm

Converts an XPLOR trajectory into a CHARMM trajectory.