2003 Volume 2 Issue 4 Pages 135-142
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.