A common, and time-consuming, task in molecular simulation is creating entries for new molecules for a given force-field. The antechamber program from the Amber suite of tools handles most of the details of this process for Amber related force-fields. However to use it with Adun its output still needs to be converted to the FFML format. We’ve added a page describing exactly how to do this here.
The next step is adding the new molecule definitions to the force-field. A problem that often raises it head is conflicts between a force-field topology file containing custom molecules and general updates for the force-field. The current cvs version of Adun now separates custom extensions from the main topology file making it much easier to add molecules – see this page for more information.