Development of Support Program for AMBER

Abstract

A support program for AMBER was developed on the basis of the biomolecular graphics program “Modrast-P". This program has three features, which are : 1) Setting up of input files for AMBER. It is easy and efficient to make input files for AMBER modules (Figure 1) by using interactive and graphical operations. 2) Molecular modeling for building the initial structure of the molecule for molecular dynamics calculation by use of the extended function of Modrast-P. 3) Animations of atomic trajectory files from molecular dynamics simulations, calculations of atom-to-atom distances and the extraction of potential energies from output files in order to draw graphs for getting quantitative information, are possible.As an example use of this program, the structure of DNA containing anthraquinone groups was simulated (Figures 2,3).This program runs on any UNIX workstations and personal computers where PC-UNIX, such as Linux, are installed.