SAAP Force Field Technology Project

Features of the program

Outline

The SAAP simulation program is composed of three layers: the interface program, the simulation program, and the data of the SAAP parameters. The interface program is written in Java language so that it can be used independent of the OS environments of the users. On the other hand, the simulation program is written in C language. This program can be run in any OS if the source codes are compiled in your computer. Thus, the interface program and the simulation program can be used separately. The schematic outline and features of the simulation program package are shown below.

Features

  • Efficient structure sampling in water by applying the replica-exchange Monte Carlo (REMC) method.
  • Easy-to-use interface on Windows PC.

  • Graphical user interface

    The interface program utilizes the protein structure display program jV (https://pdbj.org/jv/#top) developed by Kinoshita (The University of Tokyo) and Nakamura (Osaka University). The interface consists of the structure display window, the structure input and job control window, and the energy display window.

    Execution examples

    The results of the SAAP simulation for Met-enkephalin and C-peptide are shown below.

    The table below shows the required computation time for the operation. In the SAAP simulation, the execution times in ether and water are almost the same as that in vacuo.

    Examples of the stable structures obtained by using the SAAP simulation program are shown below.

    Met-enkephalin

    C-peptide

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