MOLDA for Windows - A Molecular Modeling and Molecular Graphics Program Using a VRML Viewer on Personal Computers

Hiroshi YOSHIDA and Hiroatsu MATSUURA

1. INTRODUCTION

The recent development of the Internet, especially World Wide Web (WWW), has changed the computer network and computer graphics dramatically. For three-dimensional (3D) graphics on the computer, the Virtual Reality Modeling Language (VRML) is used on the WWW. Molecular graphics using VRML has also been developed recently [5,6]. This new technique enables us not only to display molecules on the screen but also to change the point of view with respect to the object shown.

Under such circumstances, we have developed an interactive molecular modeling and molecular graphics program MOLDA for Windows, which is designed to be used as an interface to the ab initio MO program GAUSSIAN 94 [7] and the MD simulation program AMBER 4.0 [8] as well as the molecular mechanics program MM2 [4]. The 3D molecular structures in VRML format can be generated by using this program and the molecular models are exported over the Internet by using VRML.

2. IMPLEMENTATION

3. OVERVIEW OF MOLDA FOR WINDOWS AND DISCUSSION

When MOLDA is running, all of the commands of MOLDA (summarized in Table 1) are allocated to the menu bar (Fig. 1). The main feature of the molecular modeling is the same as that of MOLDA4 described previously [3] except for the use of a mouse pointing device. Using the molecular modeling functions of MOLDA, the labour involved in preparing molecular structure data for molecular science is considerably reduced. Selection of a menu activates the corresponding subcommands. Menus are listed below.

1. File Menu

The 'File' menu deals with molecular coordinate file input and output. The valid molecule file format is MODRAST/MOLDA[3,9] and MSC's XMol XYZ file format [10]. If no file format is specified, MODRAST/MOLDA file format is assumed by default. Molecular coordinates can be saved in VRML file format (See section 3.2.).

2. Edit Menu

The 'Edit' menu deals with the pasting of the Cartesian coordinates obtained from GAUSSIAN 94 or MM2. 'Undo' and 'Copy' commands are also available.

3. View Menu

The 'Edit' menu deals with the change of the screen appearance (such as showing x- and y-axes, scaling molecular size and locating the number on each atom).

Table 1. Menus/Submenus and commands in MOLDA for Windows

Menu	Submenu	Option	Description
File
	Open		Read molecular structure data in MOLDA or XMol file format
	Save		Save molecular structure data in MOLDA or XMol file format
	Save As		Save molecular structure data in MOLDA or XMol file format as specified file name
	Save in VRML		Save molecular structure data in VRML file format ( Dreiding sticks, ball-and-stick and spacefilling models are available)
	Print		Hardcopy of display
	Exit		Exit MOLDA for Windows
Edit
	Undo		Undo delete
	Copy		Copy MOLDA data to clipboard
	Paste
		MOLDA	Paste MOLDA data in clipboard on MOLDA
		MM2	Paste MM2 data in clipboard on MOLDA
		GAUSSIAN	Paste GAUSSIAN data in clipboard on MOLDA
View
	Axes		Show x- and y-axes
	Atom Number		Locate the number on each atom
	Auto Scaling		Scale the size of molecule automatically
	Cancel Atoms Automatically		Cancel duplicated atoms automatically when merged
	Cancel Bonds Automatically		Cancel duplicated bonds automatically when merged
Model
	Input
		Atom	Input the number of atoms, the Cartesian coordinate and the atomic numbers
		Bond	Generate a bond between specified two atoms
		Alkane	Make the all-trans conformation of an n-alkane molecule by input of the number of carbon atoms
		Hydrogen	Add hydrogen atoms to the carbon atoms
		a-No	Replace a specified atom by another element
	Cancel
		Atom	Delete a specified atom
		Bond	Delete a specified bond
		Component	Delete a specified group of atoms
	Merge
		Point	Place a molecule by specification of an atom so that the specified atom is at the specified position
		Atom	Replace an atom or group of atoms of the molecule by another molecule
		Bond	Connect two molecules in such a way that their specified bonds overlap
		Subst	Substitute an atom or a group of atoms with a common substituent
	Group
		Cn	Do operation Cn
		m	Do operation s
		i	Do operation i
		Sn	Do operation Sn
	Internal Rotation		Do an internal rotation around a specified bond
	Move
		Atom	Move the origin to a specified atom
		Bond	Move the origin to the midpoint of two specified atoms
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
	MM2 -> MOL		Convert MM2 output into MOLDA data
	AMBER -> MOL (Movie)		Convert AMBER trajectory file into MOLDA data as movie
	MOL -> MM2		Convert MOLDA data into MM2 input data
	MOL -> GAUSSIAN		Convert MOLDA data into GAUSSIAN 94 input data
Help
	Info		Show information of this program

Fig. 1 A menu screen of MOLDA for Windows.

4. Model Menu

The 'Model' menu deals with the construction of molecular models. The input of molecular structure is commenced with the 'Input' submenu. Input data are the Cartesian coordinates of atoms, the atomic numbers and atom connection lists, which are easily generated with mouse operation. The all-trans conformation of an n-alkane molecule can be generated in a one-step operation by using the 'Alkane' command. The input structure need only be a carbon skeleton, as hydrogen atoms can be added to the skeleton by using the 'Hydrogen' command. A specified atom may be replaced by another element by using the 'a-No.' command.

The 'Merge' submenu enables any molecules made by MOLDA to be connected with each other in several modes (a specified spatial arrangement, a substitution, a ring fusion, a bridged ring-connection and a spiro ring-connection) by mouse operation.

Another interesting feature of MOLDA is the 'Group' submenu. By using the commands in the 'group' submenu, the corresponding 'symmetry operation' can be performed. The symmetry operations are defined as follows: operation 'C6z', for example, is defined so that the molecule has a C₆ symmetry axis around the z-axis. Thus, the amount of input data may be reduced. It is worth mentioning that the construction of a complicated molecule such as coronene is greatly simplified by using this operation (Fig. 2).

Fig. 2 A coronene molecule generated by using C₆ operation.

5. Analysis Menu

The 'Analysis' menu deals with the calculation of bond distances, bond angles and dihedral angles of a molecule.

6. Convert Menu

The 'Convert' menu deals with the conversion of the Cartesian coordinates obtained by using several molecular science programs into MOLDA format file. The details are described in section 3.3.

3.2. The Feature of Molecular Graphics

The 3D molecular structures in VRML format can be generated by using MOLDA. These molecular structure data created by MOLDA or converted from GAUSSIAN 94, AMBER 4.0 and MM2 can be viewed in 3D by using a VRML viewer and demonstrated on WWW. At present, Dreiding-sticks (Fig. 3), spacefilling spheres (Fig. 4) and ball-and-stick models (Fig. 5) are available. The molecular models written in VRML can be easily operated by the VRML viewer not only by local users but also by remote users, who can use terminal computers connected to the Internet. Moreover, the molecular models can be viewed platform-independently; in other words, they can be displayed on the DOS/V, Macintosh and Unix machines.

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.

3.3. The Feature of an Interface to Molecular Science Programs

When the 'Convert' menu is selected, the data format for MOLDA and several molecular science programs is converted to each other as described below.

1. MOLDA can make input data for molecular mechanics (MM2) or ab initio MO calculations (GAUSSIAN 94). For MM2, the conversion of data for MOLDA into those for MM2 was described in detail elsewhere [3].

2. The output files of GAUSSIAN 94, AMBER 4.0 and MM2 can be converted to the data of MOLDA format. The results of MD simulations can be animated on the screen.

4. CONCLUSION

REFERENCES