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

Hiroshi YOSHIDA and Hiroatsu MATSUURA



Molecular modeling and molecular graphics using personal computers have been developed dramatically during the 1980-1990's. In the 1970's, powerful molecular modeling programs were developed only for large-scale computers [1,2]. In 1984, interactive molecular modeling programs, MOLDA and GRIMM, on personal computers for interface to molecular science were developed [3]. These programs were designed to be used as an interface to Allinger's molecular mechanics program MM2 [4], since in those days, MM2 was the most general and widely used program in chemistry. In recent years, however, ab initio molecular orbital (MO) calculations and molecular dynamics (MD) simulations have been widely used, not only in theoretical chemistry but also in organic chemistry and drug design.

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.


We used an IBM/AT compatible (DOS/V) machine, in which the Microsoft Windows95/NT3.51 operating system was installed. The MOLDA for Windows was written in Microsoft Visual Basic 4.0. A Netscape Navigator which plugged-in a Live3D was used as a VRML viewer. The DOS/V machine was connected to UNIX workstations through TCP/IP protocol. The ab initio MO program GAUSSIAN 94 and the MD simulation program AMBER 4.0 were used on these workstations.


3.1. The Feature of Molecular Modeling

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

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
UndoUndo delete
CopyCopy MOLDA data to clipboard
MOLDAPaste MOLDA data in clipboard on MOLDA
MM2Paste MM2 data in clipboard on MOLDA
GAUSSIANPaste GAUSSIAN data in clipboard on MOLDA
AxesShow x- and y-axes
Atom NumberLocate the number on each atom
Auto ScalingScale the size of molecule automatically
Cancel Atoms AutomaticallyCancel duplicated atoms automatically when merged
Cancel Bonds AutomaticallyCancel duplicated bonds automatically when merged
AtomInput the number of atoms, the Cartesian coordinate and the atomic numbers
BondGenerate a bond between specified two atoms
AlkaneMake the all-trans conformation of an n-alkane molecule by input of the number of carbon atoms
HydrogenAdd hydrogen atoms to the carbon atoms
a-NoReplace a specified atom by another element
AtomDelete a specified atom
BondDelete a specified bond
Component Delete a specified group of atoms
PointPlace a molecule by specification of an atom so that the specified atom is at the specified position
AtomReplace an atom or group of atoms of the molecule by another molecule
BondConnect two molecules in such a way that their specified bonds overlap
SubstSubstitute an atom or a group of atoms with a common substituent
CnDo operation Cn
mDo operation s
iDo operation i
SnDo operation Sn
Internal RotationDo an internal rotation around a specified bond
AtomMove the origin to a specified atom
BondMove the origin to the midpoint of two specified atoms
CoordinateGive coordinates of a specified atom
DistanceCalculate distance between two specified atoms
AngleCalculate bond angle
Dihedral AngleCalculate dihedral angle
MM2 -> MOLConvert MM2 output into MOLDA data
AMBER -> MOL (Movie)Convert AMBER trajectory file into MOLDA data as movie
MOL -> MM2Convert MOLDA data into MM2 input data
MOL -> GAUSSIANConvert MOLDA data into GAUSSIAN 94 input data
InfoShow 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.


MOLDA for Windows provides molecular graphics on the World Wide Web. The data for the molecular graphics are obtained from various programs for molecular science, such as ab initio MO, molecular dynamics and molecular mechanics calculations.


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