Analysis programs.

ANAL

is for the analysis of structure and especially molecular mechanical energy of a single configuration of a system. It can be run on structures both before and after modification by the energy programs. Running ANAL on the initial configuration of your system is a good way to locate errors in the structure that result in large energies. Anal can also be used for more sophisticated analyses of energy and structure.

CARNAL

is a molecular dynamics analysis program. It is used for geometrical measurements, root mean square coordinate fitting, trajectory averaging, and other structural analyses of MD trajectories. CARNAL executes a programming language for filtering, measuring and comparing multiple streams of coordinate files (the language contains 44 keywords and uses 10 punctuation/logical characters). As an example, one can use it to build a trajectory in which the solute is positioned for minimum root mean square fit of residues in the active site and only the first shell of waters is included.

PTRAJ

is a general purpose utility that can examine and modify prmtop files created by LEaP or PARM. It can also process trajectory files created from MD simulations, carrying out superpositions, extractions of coordinates, etc. Ptraj now can compute correlation functions, thus incorporating the capability of a variety of auxiliary programs in earlier version of Amber.

NMANAL/LMANAL

computes atomic fluctuations and various correlation functions from normal modes.

MM-PBSA

is a script that automates energy analysis of snapshots from a molecular dynamics simulation using ideas generated from continuum solvent models.