ICDA
From Jacobson Lab Wiki
ICDA (Independent Cluster Decomposition Algorithm) is a computationally efficient method of assigning polar states in proteins. It works by assuming a protein is composed of custers of non-interacting polar residues and combinatorially evaluating all the possibilities within each cluster.
The corresponding plop command for ICDA polar state assignment is pka clust.
Quick Start: To run ICDA
pka clust beg end fastpka no adjust yes
To get plop to recognize the altered protonation states, in load pdb ....
load pdb mypdb.pdb pka frompdb [other options]