基于拓扑子集的势场原子类型的派定

对于除了标准氨基酸、核酸残基以外的一般分子,派定分子中原子的原子类型,确定原子类型在不同分子势场之间的转换,这些工作一般是由人工来完成。本文从分子拓扑学的角度解析了分子势场的原子类型(atom type)定义,以基于分子拓扑子集取代原子类型定义的分子片断为途径,实现势场原子类型的计算机自动派定。该方法易于编程,并能满足用户调整原子类型的意愿。

Topology-based automatical assignment of force field atom types

For general molecules the atom types are usuallv manually assigned rather than automatically. And the conventional definition of the atom types for force fields represents structural fragments in the structure of a molecule. From the topological point of view, each of such fragments is one-to-one mapped on a topological subset of molecules of interest, which can be used as the topological definition of atom types in place of their conventional semantic definition of atom types. Based upon the topological definition, the authors in this present paper put forward an approach to the automatical assignment of atom rypes, which proves to be a favorite for the actual research practice.