next up previous contents index
Next: Parameters.clear() clear Up: The Libraries class: stereochemical Previous: read   Contents   Index

Parameters.append() -- append parameters library

This command reads the parameters from the parameter library given by file, such as the CHARMM 22 parameter file for proteins with all atoms [MacKerell et al., 1998]. The parameters are added to any already in memory. This file contains the values for bond lengths, angles, dihedral angles, improper dihedral angles, and non-bonded interactions. MODELLER relies on slightly modified CHARMM-22 parameters to reproduce the protein geometry in the MODELLER environment. For example, for the default non-hydrogen atoms model, the $ \omega $ dihedral angle restraints are stronger than the original CHARMM 22 values which apply to the all-hydrogen model. For a sparse discussion of the parameter library, see the FAQ Section 3.1, Question 8.

Note that, in contrast to older versions of MODELLER, the non-bonded spline parameters used in loop modeling are not read by this function. See instead the documentation for the separate group_restraints class, in section 6.13, for more information.

Example: See model.patch() command.

Automatic builds 2012-08-29