<scp>AMBER</scp>: Assisted model building with energy refinement. A general program for modeling molecules and their interactions

Abstract

Abstract We describe a computer program we have been developing to build models of molecules and calculate their interactions using empirical energy approaches. The program is sufficiently flexible and general to allow modeling of small molecules, as well as polymers. As an illustration, we present applications of the program to study the conformation of actinomycin D. In particular, we study the rotational isomerism about the D ‐Val‐, L ‐Pro, and L ‐Pro‐Sar amide bonds as well as comparing the energy and structure of the Sobell model and the x‐ray structure of actinomycin D.