PATCH -- patch MODEL topology

RESIDUE_IDS = <string:0>	''	identifiers of the patched residues
RESIDUE_TYPE = <string:1>	'undefined'	patching residue type
TOPOLOGY_MODEL = <integer:1>	3	selects topology library: 1-10

Description:

This command uses a CHARMM patching residue to patch the topology of the MODEL. CHARMM patch rules are observed.

RESIDUE_TYPE is the type of the patching residue (PRES entry in the topology library), such as 'DISU', 'NTER', 'CTER', etc. You do not have to apply explicitly the N- and C-terminal patches to protein chains because the 'NTER' and 'CTER' patches are applied automatically to the appropriate residue types at the termini of each chain at the end of each GENERATE_TOPOLOGY command.

RESIDUE_IDS are residue identifiers of the patched residues (Section 2.4.1). The first residue is the patched residue 1, the second residue is the patched residue 2, etc; for example, the 'DISU' patching residue has two patched Cys residues while the 'ACE' patching residue has only one patched residue. The order of the residue identifiers here has to match the definition of the patching residue in the topology library.

It is not allowed to patch an already patched residue. Since the N- and C-terminal residues of each chain are automatically patched with the 'NTER' and 'CTER' patching residues, respectively, a user who wants to patch the N- or C-terminal residues with other patches, should turn the default patching off before executing GENERATE_TOPOLOGY. This is achieved by SET PATCH_DEFAULT = off.

Example:

# Example for: PATCH, READ_TOPOLOGY, READ_PARAMETERS

# This will define a CYS-CYS disulfide bond between residues 3 and 22.

READ_TOPOLOGY   FILE = '$(LIB)/top_heav.lib'
READ_PARAMETERS FILE = '$(LIB)/par.lib'

# Read the sequence: 
READ_MODEL FILE = '1fas'
# have two copies of the sequence in the alignment, for TRANSFER_XYZ later:
SEQUENCE_TO_ALI ATOM_FILES = '1fas', ALIGN_CODES = '1fas'
SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES '1fas.ini', ;
                ALIGN_CODES = ALIGN_CODES '1fas-ini'
GENERATE_TOPOLOGY SEQUENCE = '1fas-ini'

# Create the disulfide bond:
PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '3' '22'

# Get MODEL's coordinates from the template, using the alignment (1:1 here):
TRANSFER_XYZ
# Calculate missing coordinates using internal coordinates:
BUILD_MODEL INITIALIZE_XYZ = off

# Create the stereochemical restraints
MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo'

# Calculate the energy to test the disulfide:
ENERGY