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Last Modified 7 Sep 2007 |
Molecular Modeling and Structure-based Drug Design Systems
ONIOM Interface for Receptor Compatible to the Protein Data Bank format versions 3.0 and 3.1.
Feature & Function At present, the ONIOM method of Gaussian, the MOZYME method of Mopac200X, and the ab-initio fragment MO method are the representative quantum chemistry calculations for calculating a big molecular system such as a protein molecule system. ONIOM Interface for Receptor is an interface for performing the multi-layer ONIOM calculations of Gaussian using the HyperChem. On the other hand, an interface, Mopac Interface for HyperChem, to the MOZYME method is available for HyperChem. Thus, two of three representative quantum chemistry calculation methods become available for calculating the big molecular system using the HyperChem graphical user interface. ONIOM Interface for Receptor can automatically create a Gaussian job file for performing the 2-layer (QM:QM and QM:MM) and 3-layer (QM:QM:QM and QM:QM:MM) ONIOM calculations of Gaussian using the excellent HyperChem molecular modeling functions. The results (atomic charge and the structure) of the Gaussian calculations can be reflected to the molecular system in the HyperChem workspace immediately.* The interface can deal with a molecule system, which consists of a protein and a small molecule such as a receptor and a ligand, and can automatically create the missing parameters of force field, the link atoms, and the charges.** Thus, as soon as the program is started, the Gaussian job can be initiated after several seconds without any manual parameter settings, regardless of the preparation of the job file for the 2-layer or 3-layer ONIOM calculation for the big molecular system (the program is also very useful for preparing the Gaussian job file of the UNIX 64 bit platforms.). ONIOM Interface for Receptor is an add-on program to the Peripheral Modeling Professional program with Gaussian Interface for HyperChem. Thus, this program can operate a molecular system under the quantum chemistry conditions. In the latest version, a protein molecule which covalently binds to a small molecule has been supported. See examples.
* When a checkpoint file name is specified in the Link0 entry box of ONIOM Interface for Receptor, the results such as the molecular orbitals and electrostatic potentials of the corresponding Gaussian job can be analyzed in detail, using a Gaussian viewer through the checkpoint or formcheck file prepared. ** In cases of (QM:MM) and (QM:QM:MM), only Amber force field is available for the molecular mechanics method in the low layer model chemistry.
The following figures show the results of superposition between the initial structure (red) and the optimized structure (blue). The initial structure was prepared using the Peripheral Modeling Professional program and the optimized structure was extracted from the Gaussian job file using the add-on ONIOM Interface for Receptor. The Gaussian job was performed at the 2-layer ONIOM(HF/6-31G*:Amber) model chemistry. Figure at the right hand side shows the superposition between the initial structure and the optimized structure obtained from the partial optimizations using frozen atom conditions for the heavy atoms in the low layer parts of the receptor.
Recommended Minimum System Requirements Processor: Intel Pentium III, Pentium 4, Celeron, Core2Duo, or Xeon (1GHz recommended; AMD processor is unidentified) Operating System: Microsoft Windows 95, 98, NT4, 2000, XP, or Vista* Memory (RAM): 256 MB (512 MB recommended) Video Card: OpenGL board Other: HD (30 MB for storage); CD-ROM drive; Mouse * There is a case wherein communication with HyperChem will be interrupted by operating an inactive window under the Windows Aero condition.
Software Requirements HyperChem: 6.x/7.x/8.03 (Windows version; Student edition is unidentified) Gaussian: Gaussian98W Revisoin A.9 or later (i.e. Gaussian03W recommended) is necessary to reflect the results of the Gaussian calculations to HyperChem.* TclPro1.2: TclPro1.2 (Windows version) is necessary to run ONIOM Interface for Receptor. TclPro1.2 is available on the Web free of charge. * It will be necessary to edit the created Gaussian job file in order to run on Gaussian98, because of different format (ONIOM) between Gaussian98 and Gaussian03.
Description ONIOM Interface for Receptor has been integrated to the Peripheral Modeling Professional module program in the Homology Modeling Professional for HyperChem package. Refer also to this program. ONIOM Interface for Receptor is only available for the molecule system which consists of at least one or more protein molecules and one or more non-protein molecules. The ONIOM Interface for Receptor package is made from a minimum number of the module programs in the Homology Modeling Professional for HyperChem package for performing a Gaussian job using HyperChem.
Evaluation A free package, Molecular Modeling Tools for HyperChem, is available. Please try it on evaluating our products.
* HyperChem is a registered trademark of Hypercube, Inc. ** Gaussian is a registered trademark of Gaussian, Inc.
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