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]