Last Modified

   10 April 2017

Molecular Modeling and Structure-based Drug Design Systems

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Gaussian Interface for HyperChem

Computational Chemistry Environment Based on HyperChem GUI


2017/04/10 Compatible to Gaussian16


Gaussian Interface for HyperChem


The most powerful and sophisticated molecular modeling environment

HyperChem  front-ended


The most powerful computational chemistry environment

Gaussian  back-ended



"Gaussian Interface for HyperChem" can automatically prepare a Gaussian input file, "job file", for a molecular system constructed using the powerful molecular modeling function of HyperChem. The calculation results (atomic charges and optimized structure) of the Gaussian job can be immediately reflected to the corresponding molecule in the HyperChem workspace.* The interface can prepare almost all of major methods and options except for the ONIOM method and supports the Link1 calculations of Gaussian. When a multi-step job is used, the interface can reflect these results, separately. When some molecules exist in the HyperChem workspace, the interface can treat these molecules independently or simultaneously.

Gaussian Interface for HyperChem is an add-on program to the Peripheral Modeling program of the Homology Modeling Professional for HyperChem package. Therefore, this program serves as a logical molecular modeling tool for preparing a small molecule in a biological macromolecular system, as well as can be used for obtaining the chemical properties of a simple small molecule. When the interface is used for a biological macromolecular system including some small molecules, the interface can provide a simple, high-speed, and highly precise method for preparing the atomic charges for the entire system instead of the QM/MM method such as the ONIOM method (see the advanced usages and tutorial).

The full-automatic ONIOM Interface to the ONIOM method of Gaussian is also available from the Peripheral Modeling program of the Homology Modeling Professional for HyperChem package.

ONIOM Interface


Additional Functions

Moreover, since HyperChem carries a Z-matrix interface for Mopac5, 6, and 7 in default, their Gaussian jobs can be initiated using Gaussian Interface for HyperChem without any conversions to the corresponding internal coordinate. If Q-Chem for Windows and a set of MOPAC2000 and Mopac Interface for HyperChem are available, the HyperChem - Gaussian - Mopac - Q-Chem compatibility becomes possible on the HyperChem graphical user interface, thus giving a powerful computational chemistry environment.


* When a checkpoint file name is specified in the Link0 entry box of Gaussian Interface for HyperChem, the results of the corresponding Gaussian job can be analyzed in detail, using a Gaussian viewer through the checkpoint or formcheck file prepared.



Motonori Tsuji, Molecular Science. 1, NP004, 2007.

Science319, 624-7, 2008.

Biochemical and Biophysical Research Communications. 339, 173-177, 2010.

Biochemistry. 49, 10647-10655, 2010.

Plant Cell Physiol. 53, 1638-1647, 2012.

Motonori Tsuji, Journal of Structural Biology. 185, 355-365, 2014.

Motonori Tsuji, et. al., Journal of Computer-Aided Molecular Design. 2015, 29, 975-988.

Motonori Tsuji, Journal of Molecular Graphics and Modelling. 2015, 62, 262-275.

Motonori Tsuji, et. al., FEBS Open Bio. 2017, 7, 391-396, DOI: 10.1002/2211-5463.12188.


Recommended Minimum System Requirements

Processor: Intel Pentium III, Pentium 4, Celeron, Core2Duo, Xeon, or later (1GHz recommended)

Operating System: Microsoft Windows 95, 98, NT4, 2000, XP, Vista, 7, 8.x and 10 (32 bit or 64 bit version)

Memory (RAM): 256 MB (512 MB recommended)

Video Card: OpenGL board

Other: HD (30 MB for storage); CD-ROM drive; Mouse


Software Requirements

HyperChem: 5.x/6.x/7.x/8.x (Windows version)

Gaussian: Gaussian98W Revisoin A.9 or later (i.e. Gaussian03W, 09W, or 16W (32bit or 64bit, Single- or Multi-Processor version))

TclPro1.2: TclPro1.2 (Windows version) is necessary to run Gaussian Interface for HyperChem. TclPro1.2 is available on the Web free of charge.



Compatible to the Protein Data Bank format versions 3.0-3.3.

Gaussian Interface for HyperChem has been integrated to the Peripheral Modeling module program in Homology Modeling Professional for HyperChem. Refer also to the Peripheral Modeling module program.




* HyperChem is a registered trademark of Hypercube, Inc.

** Gaussian is a registered trademark of Gaussian, Inc.



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