This is part of the isdb module

Bayesian refinement of AF models.

This action implements the Bayesian approach to refine AF models introduced here and here. It can be used to generate conformational ensembles of IDPs or refine AF models prior to small-molecule virtual screening.

Examples

Examples

Complete tutorials can be found here and here.

Glossary of keywords and components

Description of components

By default this Action calculates the following quantities. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity	Description
ene	Bayesian bAIes energy

The atoms involved can be specified using

ATOMS

atoms used in the calculation of bAIes energy. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Compulsory keywords

DATA_FILE	file with AF2 fit parameters
PRIOR	type of prior to use (NONE, JEFFREYS, CAUCHY

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances
TEMP	temperature in kBt units
SIGMA_MIN	minimum value of sigma