AMBER 2015 LONDON WORKSHOP - HANDS ON ANALYSIS SESSION

Thomas E. Cheatham III, Christina Bergonzo, Daniel Roe, & Rodrigo Galindo-Murillo

• AMBER CPPTRAJ tutorial 0 from ambermd.org - Basics and interactive use of CPPTRAJ

• AMBER CPPTRAJ tutorial 1 from ambermd.org - RMSD fitting and fits to reference structures that may have a different number of atoms or topology

• DNA-tutorial with some additional basic analyses

• Principal component analysis

• Cluster and combined cluster analysis

• Hydrogen bond analysis

• Replica exchange analysis

Copyright Thomas E. Cheatham III, Christina Bergonzo, Daniel Roe & Rodrigo Galindo-Murillo, 2015