patches

A patches directive is used to specify patches, which are changes to single amino acid residues enabled by the CHARMM36 topologies. The syntax for specifying a patch is as follows:

<patchname>:<chain>:<seqnum>

<patchname> is the CHARMM36 patch name, <chain> is the chain ID, and <seqnum> is the residue number. For example, if you wanted to protonate an aspartate at position 12 in chain A, your patches mod directive would look like this:

patches:
  - ASPP:A:12

ASPP is the CHARMM36 patch name for protonating an aspartate, A is the chain ID, and 12 is the residue number. This will apply the specified patch to the residue at that position in the specified chain.