Development of an Assisting System to Add New Residues to the Standard AMBER Residue Database

Kazuhiro SASAa*, Takeshi UNOb, Haruhisa HAYASHIa, Kazushige YAMANAa and Hidehiko NAKANOa

aDepartment of Materials Science and Chemistry, Graduate School of Engineergin, Himeji Institute of Technology
2167 Shosha, Himeji, Hyogo, 671-2201, JAPAN
bDepartment of Management and Information Sciences, Hiroshima Prefectural University
562 Nanatsuka, Shobara, Hiroshima, 727-0023, JAPAN

(Received: June 3, 2003; Accepted for publication: July 18, 2003; Published on Web: November 20, 2003)

AMBER (Assisted Model Building with Energy Refinement) is a powerful tool for simulations of bio-molecules and so on. To simulate DNA molecules with new residues that are not registered in the AMBER database, it is necessary to register them on this database by using one of the AMBER modules, PREP. However, the format of the PREP input file is very complicated, and it is hard to make by hand. Therefore, in this work, in order to make the PREP input file interactively with visualization, we add a function to our molecular structural display system, "Modrast-P". By using this function, the PREP input file can be made easily and efficiently.

Keywords: DNA, AMBER, PREP, Modrast-P, Molecular dynamics


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