|
|
|
Last Modified 7 Sep 2007 |
Molecular Modeling and Structure-based Drug Design Systems
Peripheral Modeling Professional for HyperChem* with Gaussian Interface for HyperChem & ONIOM Interface for Receptor
In this professional program, in addition to all functions of the Peripheral Modeling module program in the Homology Modeling for HyperChem package, the structures optimized by Gaussian can be reflected to the corresponding molecules in the HyperChem workspace using the RMS fitting technique (in the normal version in the Homology Modeling for HyperChem package, the structures optimized by Gaussian can be reflected to the molecules in the HyperChem workspace, only when these molecules are non-protein molecules.). Moreover, in this professional version, ONIOM Interface for Receptor is available for a molecule system, which consists of a protein molecule and a small molecule such as a receptor and a ligand. ONIOM Interface for Receptor can automatically create a Gaussian job file for the 2-layer (QM:QM and QM:MM) and 3-layer (QM:QM:QM and QM:QM:MM) ONIOM calculations and the result can be reflected to the molecule system in the HyperChem workspace. Thus, as soon as the interface 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 can reflect some kind of atomic charges and the structures in the optimization processes or the structure optimized. Additionally, this program supports the "UNDO" function for the structural modifications, i.e., the program can revert to the original structure from the structures optimized using the HyperChem geometry optimizations, the structures reflected using Gaussan Interface for HyperChem, and the structures reflected using ONIOM Interface for Receptor.
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 (1 GHz recommended; AMD processor is unidentified) Operating System: Microsoft Windows 95, 98, NT4, 2000, XP, or Vista Memory (RAM): 256 MB (512 MB recommended) Other: HD (30 MB for storage); CD-ROM drive; Mouse
Software Requirements HyperChem*: 5.x/6.x/7.x/8.03 (Windows version; Student edition is unidentified) The version 6.x or later is necessary to run ONIOM Interface for Receptor. Gaussian**: Gaussian98W Revisoin A.9*** or later (i.e. Gaussian03W recommended) is necessary to run Gaussian Interface for HyperChem and ONIOM Interface for Receptor. TclPro1.2: TclPro1.2 (Windows version) TclPro1.2 is available on the Web free of charge.
Description 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.
* HyperChem is a registered trademark of Hypercube, Inc. ** Gaussian is a registered trademark of Gaussian, Inc. *** 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.
|
|
Site Map |
