This creates a new class to be used for scoring models with the GB/SA implicit solvation model. To activate scoring, you must add an instance of this class to the relevant energy_data.energy_terms list, in the same way as for user-defined energy terms (see Section 7.1.3).
library is the name of a library file containing radii and solvation parameters for all atom types. solvation_model selects which column of solvation parameters to use from this file. cutoff sets the distance in angstroms used to calculate the Born radii; the calculation can be made faster at the expense of accuracy by using a smaller cutoff. Note that GB/SA uses the same nonbonded list as the other dynamic terms, so cutoff should be chosen to be no greater than energy_data.contact_shell. The electrostatic component of GB/SA is also switched using the value of energy_data.coulomb_switch.
# Example for: gbsa.scorer() # This will calculate the GB/SA implicit solvation energy for a model. from modeller import * from modeller import gbsa from modeller.scripts import complete_pdb env = environ() env.io.atom_files_directory = ['../atom_files'] env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') # Calculate just the GB/SA score; turn off soft-sphere env.edat.dynamic_sphere = False env.edat.energy_terms.append(gbsa.Scorer()) # GB/SA falls off slowly with distance, so a larger cutoff than the # default (4.0) is recommended env.edat.contact_shell = 8.0 mdl = complete_pdb(env, "1fas") # Select all atoms atmsel = selection(mdl) # Calculate the energy atmsel.energy()
Automatic builds 2019-06-19