Preparation of Solutes¶
Similar to monomer_prep, we annotate solute topologies to aid specific calculations. At present these annotations are only needed to label solute atoms involved in hydrogen bonding.
Summary of Annotations¶
| Symbol | Description | More info |
|---|---|---|
| H | Specifies a hydrogen that can participate in a hydrogen bonding interaction | Hydrogen Bonding |
| D | Specifies a hydrogen bond donor atom | Hydrogen Bonding |
| A | Specifies a hydrogen bond acceptor atom | Hydrogen Bonding |
Hydrogen Bonding¶
In order to identify hydrogen bonds in a trajectory, one must specify which hydrogen atoms are able to participate in such an interaction as well as which atoms are hydrogen bond donors and which are hydrogen bond acceptors.