enm

Elastic Network Models

A collection of tools for working with ENMs, found in the Packages/ElasticNetworks/ directory:

anm

Computes the anisotropic network model for a structure. Reference: Atilgan, et al., Biophys. J. 80, 505-515, (2001).

gnm

Computes the gaussian network model for a structure. Reference: Bahar, et al, Folding and Design 2, 173-181, 1997.

vsa

Computes the vibrational subsystem analysis model for a structure. Reference: Woodcock, et al, J. Chem. Phys., 129, 214109-9, 2008

psf-masses

Copies atom masses from a PSF into the occupancy field of a PDB

heavy-ca

Places the total mass for a residue into its CA (for a PDB with masses)

enmovie

Creates a DCD depicting motion along the axes taken from an ENM result

flucc2b

Computes B-values based on ENM (now deprecated)

eigenflucc

Computes the fluctuations from either ENM or PCA output. These can be mapped to B-values in a structure.

Important note

The ENM tools return all eigenpairs, including the zero-modes. The results are ordered such that the first 6 entries correspond to the zero modes in a typical case. This means that when you specify a mode to subsequent analysis tools (such as porcupine or eigenflucc), you must account for this (i.e. add 6 to the mode requested).