This page describes how to:
- Extend a force-field with new molecules
- Override molecules with custom entries
without having to modify the main FFML topology file for the force-field. It assumes you already have a valid FFML file for the new molecules – if you don’t see this page for how to create one.
Extending a force-field in this way requires placing valid a FFML topology file in a specific location on the file system. There are two choices for the location
The first is for user specific customizations. The second can be used to add new entries for all users on a given computer.
$USER_LIBRARY_DIR is $HOME/Library on Mac and (usually) $HOME/GNUstep/Library/ on linux. $SYSTEM_LIBRARY_DIR is /Library on Mac and (again usually) /usr/GNUstep/System/Library/ on linux. $FORCE-FIELD_NAME is the name of the force-field being extended.
So if you want to add new molecules to Amber96 on Mac just for yourself then the path would be
Once this folder is created simply copy an FFML topology file to it. Any number of FFML files can be added to the directory, and each can contain any number of molecules. The only requirements are that each FFML topology file has a single <moleculeclass> element which contains all the molecules, and that the value of the <forcefield> element in the FFML file matches the folder it has been placed in.
When this force-field is selected in the system builder Adun will automatically add all the custom entries to it. If one of the custom entries defines a molecule with the same name as a molecule in the main force-field file, the custom entry overrides the original entry.