1. File Menu
The 'File' menu deals with molecular coordinate file input and output. MOLDA [2,3], XMol XYZ [4] and Protein Data Bank [5] format files can be read. Molecular coordinates can be saved in VRML1.0/2.0 file formats (See section 3.2.).
2. View Menu
The 'View' menu deals with the change of the screen appearance (such as showing x- and y-axes and locating the number on each atom).
3. Model Menu
The 'Model' menu deals with the construction of molecular models. The all-trans conformation of an n-alkane molecule can be generated in a one-step operation by using the 'Input alkane' command (Fig. 1). A specified atom may be replaced by another element by using the 'Input a-No.' command. 'Internal rotation' can also be available (Fig. 2). The 'Merge subst' menu enables any molecules created by MOLDA to be connected with each other by mouse operation.
4. Analysis Menu
The 'Analysis' menu deals with the calculation of bond distances, bond angles and dihedral angles of a molecule.
5. Convert Menu
The 'Convert' menu deals with the conversion of the Cartesian coordinates obtained by using MOLDA into MOPAC and GAUSSIAN 94 input data formats. The details are described in section 3.3.
Table 1. Menus/submenus and commands in MOLDA for Java
Menu/Submenu/Command | Description | |
---|---|---|
File | ||
Open | Read molecular structure data in MOLDA file format | |
Save As | Save molecular structure data in MOLDA file format as specified file name | |
Import XMol | Import molecular structure data in XMol file format (*.xyz) | |
Import PDB | Import molecular structure data in PDB file format (*.pdb) | |
Import MOPAC | Read the MOPAC output coordinates | |
Import GAUSSIAN | Read the “Standard Orientation” geometry from GAUSSIAN output file | |
VRML1.0 (Dreiding sticks) | Save molecular structure data in VRML1.0 file format (Dreiding stick model) | |
VRML1.0 (Ball and stick) | Save molecular structure data in VRML1.0 file format (Ball and stick model) | |
VRML1.0 (Space filling) | Save molecular structure data in VRML1.0 file format (Space-filling model) | |
VRML2.0 (Dreiding sticks) | Save molecular structure data in VRML2.0 file format (Dreiding stick model) | |
VRML2.0 (Ball and stick) | Save molecular structure data in VRML2.0 file format (Ball and stick model) | |
VRML2.0 (Space filling) | Save molecular structure data in VRML2.0 file format (Space-filling model) | |
View | ||
Axes | Show x- and y-axes | |
Atom number | Locate the number on each atom | |
Generate bonds automatically | Generate bonds automatically | |
Model | ||
Input bond | Generate a bond between two specified atoms | |
Input alkane | Make the all-trans conformation of an n-alkane molecule by input of the number of carbon atoms | |
Input a-No. | Replace a specified atom by another element | |
Cancel atom | Delete a specified atom | |
Cancel bond | Delete a specified bond | |
Merge subst | Substitute an atom or a group of atoms with a common substituent | |
Internal rotation | Do an internal rotation around a specified bond by dragging a mouse | |
Analysis | ||
Coordinate | Give coordinates of a specified atom | |
Distance | Calculate distance between two specified atoms | |
Angle | Calculate bond angle | |
Dihedral Angle | Calculate dihedral angle | |
Convert | ||
MOLDA -> MOPAC | Convert MOLDA data into MOPAC input data | |
MOLDA -> GAUSSIAN | Convert MOLDA data into GAUSSIAN 94 input data | |
Help | ||
Info | Show information of this program |
Fig. 1 A hexane molecule created by 'Input alkane' menu. | Fig. 2 Do an internal rotation by 'Internal rotation' menu. |
Fig. 3 A Dreiding stick model of 18-crown-6.
Fig. 4 A Space-filling model of 18-crown-6.
Fig. 5 A Ball and stick model of 18-crown-6.
Fig. 6 Creating GAUSSIAN 94 input data.