MAKE_TOPOLOGY_MODEL -- make a subset topology library

TOPOLOGY_MODEL = <integer:1>

3

selects topology library: 1-10

Description:

This command makes a residue topology library from the most detailed CHARMM topology library, which contains all atoms, including all hydrogens (corresponding to TOPOLOGY_MODEL = 1). There are currently ten residue topologies, all of which are defined in library $MODELS_LIB. For example, the default non-hydrogen atom topology is selected by TOPOLOGY_MODEL = 3. For each TOPOLOGY_MODEL and residue type, the $MODELS_LIB library lists those atoms in the full atom set that are part of the specified topology. This command works by deleting all the entries that contain non-existing atoms from the original topology file. 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. TOPOLOGY_MODEL must be an integer from 1 to 10. For more information about the topology library, see the FAQ Section 1.8, Questions 17 and 18.

Example:

# Example for: MAKE_TOPOLOGY_MODEL, WRITE_TOPOLOGY_MODEL

# This creates a topology library for heavy atoms from the 
# CHARMM all-atom topology library:

# Read CHARMM all-atom topology library:
READ_TOPOLOGY FILE = '${LIB}/top.lib'

# Keep only heavy atoms (TOPOLOGY_MODEL = 3)
MAKE_TOPOLOGY_MODEL TOPOLOGY_MODEL = 3

# Write the resulting topology library to a new file:
WRITE_TOPOLOGY_MODEL FILE = 'top_heav.lib'