PATCH_SS_TEMPLATES -- guess MODEL disulfides from templates

ALIGN_CODES = $\langle{\tt string:0}\rangle$	'all'	codes of proteins in the alignment
ATOM_FILES = $\langle{\tt string:0}\rangle$	''	complete or partial atom filenames
ATOM_FILES_DIRECTORY = $\langle{\tt string:1}\rangle$	'./'	input atom files directory list (e.g., 'dir1:dir2:dir3:./:/')
WATER_IO = $\langle{\tt logical:1}\rangle$	off	whether to read water coordinates
HETATM_IO = $\langle{\tt logical:1}\rangle$	off	whether to read HETATM coordinates
HYDROGEN_IO = $\langle{\tt logical:1}\rangle$	off	whether to read hydrogen coordinates
TOPOLOGY_MODEL = $\langle{\tt integer:1}\rangle$	3	selects topology library: 1-9

Requirements:

alignment

Output:

DISTANCE_ATOMS

Description:

This command defines and patches disulfide bonds in the MODEL using an alignment of the MODEL sequence with one or more template structures. The MODEL sequence has to be the last sequence in the alignment. The template structures are all the other proteins in the alignment. All Cys-Cys pairs in the target sequence that are aligned with at least one template disulfide are defined as disulfide bonds themselves. The covalent connectivity is patched accordingly.

If no alignment exists, a default 1:1 alignment is constructed. Variable ATOM_FILES can be used to specify template structures.

This command should be run after GENERATE_TOPOLOGY and before MAKE_RESTRAINTS to ensure that the disulfides are restrained properly by the bond length, angle, and dihedral angle restraints and that no SG-SG non-bonded interactions are applied.

The disulfide bond, angle and dihedral angle restraints have their own physical restraint type separate from the other bond, angle and dihedral angle restraints (Table 2.4).

DISTANCE_ATOMS becomes CA SG.

Example:

# Example for: PATCH_SS_TEMPLATES and PATCH_SS_MODEL

# This will patch CYS-CYS disulfide bonds using disulfides in aligned templates:

SET OUTPUT_CONTROL = 1 1 1 1 1

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

# Read the sequence, calculate its topology, and coordinates:
READ_ALIGNMENT FILE = 'toxin.ali', ALIGN_CODES = '2ctx' '2abx' 
# Superpose the two template structures without changing the alignment.
# This is for TRANSFER_XYZ to work properly. It relies on not reading
# the atom files again before TRANSFER_XYZ.
MALIGN3D FIT = off  # This is for TRANSFER_XYZ to work properly.
READ_ALIGNMENT FILE = 'toxin.ali', ALIGN_CODES = ALIGN_CODES '1fas'
GENERATE_TOPOLOGY SEQUENCE = '1fas'
TRANSFER_XYZ
BUILD_MODEL INITIALIZE_XYZ = on
WRITE_MODEL FILE = '1fas.noSS'
# Create the disulfide bonds using equivalent disulfide bonds in templates:
PATCH_SS_TEMPLATES

# Create the stereochemical restraints
MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo'

# Calculate energy to test the disulfide restraints (bonds, angles, dihedrals):
ENERGY

READ_MODEL  FILE = '1fas.noSS'
# Create the disulfide bonds guessing by coordinates
PATCH_SS_MODEL

# Create the stereochemical restraints
MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo'

# Calculate energy to test the disulfide restraints (bonds, angles, dihedrals):
ENERGY