Construction of Ligands

Abstract

In contrast to proteins whose structures may be retrieved from extensive databases or by homology modeling, ligands are to be built up manually. Among the large number of editors to execute this task some public domain software is mentioned. To do a molecular dynamics calculation the appropriate parameter files have to set up. Using the software package GROMACS the process to gain a geometry and a topology file with the help of the PRODRG server is discussed in detail for ethanol and dobutamine. In order to facilitate the task for the user an extensive instruction is presented in conjunction with a commented exercise.