Introduction to gOpenMol
gOpenMol started as the graphical interface to the OpenMol
set of programs but is today an independent toolbox for
the display and analysis of results from a wide range of computational chemistry
programs.
gOpenMol features include:
- for the static display of molecular structures
- for the analysis and display of molecular dynamics trajectories
- the display of molecular orbitals, electron densities
- electrostatic potentials from programs like the GaussianXX, GAMESS, TurboMole
- electrostatic potentials from the UHBD (University of Houston
Brownian Dynamics)
Software:
gOpenMol can import, display and analyze several different input coordinate
file formats and binary trajectory file formats.
The program has a graphical
user interface (GUI) and an internal line command interpreter based on the
Tcl/Tk interpreter. More details about the Tcl/Tk scripting language can be found
at the address:
http://dev.scriptics.com
gOpenMol can be used for a wide range of analysis and display tasks like the
display of isocontour surfaces and cross sections of grid data.
Hardware:
gOpenMol graphics is implemened using the OpenGL
(http://www.opengl.org) or MESA
(http://www.mesa3d.org) graphics
libraries. 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 two promary hardware platforms:
- PC/Linux (MESA/OpenGL)
- Windows (WIN32)
However gOpenMol has been running on the following platforms during the develoment
phases.
- SGI IRIX (OpenGL and MESA)
- DEC Unix (MESA)
- IBM AIX (OpenGL and MESA)
gOpenMol should run on any Unix platform without any changes.
Possibilities:
gOpenMol is hopefully a multipurpose program. Currently the program
has most of the molecular dynamics analysis features of SCARECROW and a lot
of new features. Currently gOpenMol supports a wide range of molecular
coordinate input formats:
- ADF output log file
- Amber (close to the PDB format)
- CHARMm/CHARMM
- DL_Poly CONFIG file
- A frame from a trajectory
- Gaussian formatted checkpoint file
- GROMACS
- GROMOS
- HyperChem
- Insight (car files)
- Mol2
- Mumod
- OpenMol (center binary file)
- PDB (Brookhaven Protein Data Bank format)
- Tinker coordinate file
- Xmol xyz coordinate file
- XYZ general xyz coordinate file
- YASP
gOpenMol supports the following binary trajectory formats:
- Amber. Program included for the unformatting of formatted AMBER
trajectories.
- Cerius2
- CHARMm/CHARMM. Program included for the formatting/unformatting
of CHARMm/CHARMM trajectories.
- Discover
- DL_Poly
- GROMACS
- Gromos (Supporting the old GROMOS format)
- HyperChem (I haven't tested with the latest version)
- MUMOD
- XPLOR
- YASP
and the following ascii trajectory format:
- 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 isocontour surfaces and cut planes for:
- Orbitals, densities ... from GAUSSIANXX set of programs.
- Connolly type of surfaces using the ProbeSurf program.
Utility programs
All these executable programs are located in the bin/ directory and
the source code is in the utility/ directory.
- ambera2b
- Converts a formatted ascii AMBER trajectory into a unformatted one.
gOpenMol can only handle unformatted AMBER trajectories.
- charmmtrj
- This program makes the formatted/binary tranformation for a CHARMM
dynamics trajectory file.
- contman
- Performs a variety of operations on a contour (plt) file.
- convert
- Converts the output search results (FDAT) from Cambridge Structural
Database into separate PDB files.
- gcube2plt
- Converts a cube file from the GaussianXX program into a binary format
known by gOpenMol.
- gridasc2plt
- Converts a UHBD formatted PHI grid file into the plt format used by
the gOpenMol progra,
- gridbin2plt
- Converts a UHBD unformatted PHI grid file into the plt format used by
gOpenMol.
- 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 an other.
- 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.