Martinize 2 workflow¶
Martinize 2 is the main command line interface entry point for vermouth. It does many interesting things which will be explained here later, and in the end you should end up with a topology for your system. Graph central in atom recognition/identification
Pipeline¶
Make bonds¶
Repair graph¶
Resolution transformation¶
Apply Links¶
Post processing¶
Important command line options¶
Martinize2 CLI options