submodel = <int:1> | submodel to make |
This command works by deleting all the entries that contain non-existing atoms from the original topology file. The charge of each removed atom is redistributed equally between the atoms directly bonded to it (if any of these atoms is in turn marked for deletion, the charge is instead placed on that atom's bonded neighbors, and so on). Any remaining charge is then spread around the entire residue, in proportion to the absolute charge of each atom.
One must carefully test topology files produced in this way. Library $RADII_LIB must specify atomic radii for each atom in each residue type for each topology model. submodel must be an integer from 1 to 10. On exit from this routine, topology.submodel is set to submodel.
For more information about the topology library, see the FAQ Section 1.8, Questions 10 and 11.
# Example for: topology.make(), topology.write() # This creates a topology library for heavy atoms from the # CHARMM all-atom topology library: env = environ() tpl = env.libs.topology # Read CHARMM all-atom topology library: tpl.read(file='${LIB}/top.lib') # Keep only heavy atoms (TOPOLOGY_MODEL = 3) tpl.make(submodel=3) # Write the resulting topology library to a new file: tpl.write(file='top_heav.lib')