(Received: November 22, 2007; Accepted for publication: February 7, 2008)
A GUI (Graphic User Interface) for GAMESS / FMO (Fragment MO method) calculation was developed and implemented on Facio, the pre/post-processor for computational chemistry. By using this GUI, one can easily make FMO fragments for a given protein or nucleic acid and generate FMO input files.
Besides automatic fragmentation, one can manually define additional FMO fractioning points to non-peptide moiety of conjugated protein. For manual definition, a novel local structure viewer was also developed. The desired local structure is defined by an atom number or by a fragment number. Using this local structure viewer, one can check the structural validity of each FMO fragment and perform manual definition of additional fractioning points on the fragment. Manually defined fractioning points can be saved as "fragment definition file", which can be loaded later to set the predefined fractioning points.
For the optimization of hydrogen atoms automatically added to the PDB file of a protein or nucleic acid which lacks hydrogen atoms, a fragment optimization function was implemented for the GUI. While a molecular dynamics method or molecular mechanics method is usually used for this purpose, the new optimization method utilizes a molecular orbital method, such as PM3 or STO-3G of GAMESS.
Keywords: FMO, Fragment MO, GAMESS, Computational chemistry, GUI
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