gOpenMol 3.0.0

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.<br />gOpenMol can be used for the display and analysis of<br /><br /> * molecular structures and properties calculated with external programs,<br /> * molecular dynamics trajectories,<br /> * isocontour surfaces of grid data, such as molecular orbitals and electron densities.<br /> * 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. <br /><br /> * 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. <br /><br />Supported file formats<br />gOpenMol supports the following molecule coordinate input formats...<br /><br /> * ADF output log file<br /> * CHARMm/CHARMM<br /> * Chemical Markup Language (CMLTM)<br /> * Chem3D binari file<br /> * DL_Poly CONFIG file<br /> * A frame from a trajectory<br /> * Gamess DAT, IRC and LOG output files<br /> * Gaussian formatted checkpoint file<br /> * GROMACS<br /> * GROMOS<br /> * HyperChem<br /> * Insight (car files)<br /> * Mol2<br /> * Mopac<br /> * Mumod<br /> * OpenMol (center binary file)<br /> * PDB (Brookhaven Protein Data Bank format)<br /> * Spartan binary file<br /> * Tinker coordinate file<br /> * Turbomole grid file<br /> * UHBD qcd coordinate file<br /> * Xmol xyz coordinate file<br /> * GXYZ general xyz coordinate file<br /> * YASP <br /><br />... binary trajectory formats...<br /><br /> * Amber<br /> * Cerius2<br /> * CHARMm/CHARMM<br /> * Discover<br /> * DL_Poly<br /> * GROMACS<br /> * Gromos (mind you, this is the old GROMOS format)<br /> * HyperChem (This format has not yet been tested with the latest version.)<br /> * MUMOD<br /> * XPLOR<br /> * YASP <br /><br />... and ascii trajectory formats.<br /><br /> * DL_Poly trajectory format<br /> * GROMOS96 trajectory format<br /> * TINKER multi frame coordinate trajectory format<br /> * XMOL xyz multi-step data sets. The included Xvibs program enables the display of vibrational modes from the GAUSSIANXX and GAMESS programs. <br /><br />Extensive display of isocontour surfaces and cut planes for<br /><br /> * Orbitals, densities ... from GAUSSIANXX set of programs.<br /> * Connolly type surfaces using the ProbeSurf program. <br /><br />Utility programs<br /><br />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.<br />Programs that can be run through the menu Run in the GUI-window.<br /><br /> AutoDock2plt<br /> Converts an AutoDock map file to a plt file. <br /> ContMan<br /> Contour (plt) files can be manipulated by adding or substracting two contours. <br /> Gamess2plt<br /> Converts a Gamess "cube" PUNCH file to a plt file. <br /> gCube2plt/g94cub2plt<br /> Converts a cube file from the GaussianXX program into a binary format known by gOpenMol. <br /> Jaguar2plt<br /> Converts a Jaguar plot file to a gOpenMol plt file. <br /> Join Gamess IRC files<br /> Joins frames from an IRC calculation to amn XMOL file. <br /> Kont2plt<br /> Converts a Grid data file to a formatted or an unformatted plt file. <br /> Pltfile<br /> 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. <br /> Probesurf (Connolly)<br /> Generates a Connolly type of surface around the molecular system. <br /> Socket server/client<br /> Bits and pieces to send structures between two gOpenMol programs. <br /> TMole2plt<br /> Converts a TurboMole grid file to a plt file. <br /> UHBD2plt<br /> Converts a UHBD formatted and unformatted PHI grid files into the plt format used by the gOpenMol program. <br /> Xvibs (conversion)<br /> Program to generate a multi structure XMOL file for animation from a variety of quantum chemistry programs. <br /><br />Programs that can be run in a DOS-window.<br /><br /> ambera2b<br /> Converts a formatted ascii AMIER trajectory into an unformatted one. gOpenMol can handle only unformatted AMIER trajectories. <br /> charmmtrj<br /> This program makes the formatted/binary tranformation for a CHARMM dynamics trajectory file. <br /> convert<br /> Converts the output search results (FDAT) from Cambridge Structural Database into separate PDI files. <br /> MolPro<br /> 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. <br /> sybyl2amber<br /> Converts a formatted ascii Sybyl trajectory into an unformatted AMBER one. <br /> trajmerge<br /> Merges two CHARMM trajectory files into one. <br /> xplor2charmm<br /> Converts an XPLOR trajectory into a CHARMM trajectory.

Requirements:	No special requirements
Platforms:	*nix, Linux
Keyword:	Ascii,  Binary,  Charmm,  Converts,  Coordinate,  Files,  Format,  Formatted,  Gamess,  Gopenmol,  Molecular,  Poly,  Program,  Programs,  Structures,  Surfaces,  Trajectory,  Unformatted,  Utility
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