ROTATE_DIHEDRALS -- change dihedral angles

DIHEDRALS = $\langle{\tt string:0}\rangle$	'PHI' 'PSI' 'CHI1' 'CHI2' 'CHI3' 'CHI4'	dihedral angle type selection: 'phi' | 'psi' | 'omega' | 'chi1' | 'chi2' | 'chi3' | 'chi4' | 'chi5' | 'alpha'
CHANGE = $\langle{\tt string:1}\rangle$	'RANDOMIZE'	what to do: 'RANDOMIZE' | 'OPTIMIZE'
DEVIATION = $\langle{\tt real:1}\rangle$	0.0	amplitude of dihedral angle randomization
RAND_SEED = $\langle{\tt integer:1}\rangle$	-8123	random seed from -50000 to -2

Requirements:

for CHANGE='OPTIMIZE': topology & MODEL & restraints
for CHANGE='RANDOMIZE': topology & MODEL

Description:

This command changes the dihedral angles in MODEL.

CHANGE selects an optimization (when equal to 'OPTIMIZE') or randomization (when equal to 'RANDOMIZE'):

1. When optimizing, this command finds the first selected restraint that restrains the specified dihedral angle of each selected residue. It then sets the value of that dihedral to the most likely value. A residue is selected if any of its atoms is in the set 1 of selected atoms.

2. When randomizing, the command changes the specified dihedral angle of each selected residue by adding a random value distributed uniformly from $-{\sf DEVIATION}\index{DEVIATION@{\sf DEVIATION}}$ to $+{\sf DEVIATION}\index{DEVIATION@{\sf DEVIATION}}$ degrees. The value of the random seed variable, RAND_SEED, is changed after returning from the RANDOMIZE command. Use a negative integer from $-2$ to $-50000$ as the seed for the random number generator.

DIHEDRALS can be either a vector of dihedral angle names or a single string containing all the dihedral angle names separated by blanks. The dihedral angles involved in cyclic structures are not changed (e.g., sidechain dihedral angles in disulfide bonds and prolines). The dihedral angles that can be changed are listed at the top of the $RESDIH_LIB library: alpha, phi, psi, omega, chi1, chi2, chi3, chi4, chi5. Dihedral angle 'alpha' is the virtual ${C}_\alpha$ dihedral angle defined by four consecutive ${C}_\alpha$ atoms.

The bond connectivity of the MODEL has to exist before this command is executed. If you read in the model by READ_MODEL, the bond connectivity is defined by subsequent calls to READ_TOPOLOGY and GENERATE_TOPOLOGY (also make sure that SEQUENCE entry does not exist in the alignment or that no alignment is in memory).

Example:

# Example for: ROTATE_DIHEDRALS

# This will optimize and randomize dihedrals in a MODEL

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

# Select dihedral angle types for optimization and randomization:
SET DIHEDRALS = 'phi psi omega chi1 chi2 chi3 chi4 chi5'

# Read the sequence, get its topology and coordinates:
READ_MODEL FILE = '1fas'
SEQUENCE_TO_ALI ALIGN_CODES = '1fas', ATOM_FILES = ALIGN_CODES
SEQUENCE_TO_ALI ADD_SEQUENCE = on, ALIGN_CODES = ALIGN_CODES '1fas_ini', ATOM_FILES = ALIGN_CODES
GENERATE_TOPOLOGY SEQUENCE = '1fas_ini'
TRANSFER_XYZ
BUILD_MODEL INITIALIZE_XYZ = off
ROTATE_DIHEDRALS CHANGE = 'RANDOMIZE', RAND_SEED = -2312, DEVIATION = 90.0
WRITE_MODEL FILE = '1fas.ini1'

# Get restraints from somewhere and optimize dihedrals:
MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo'
ROTATE_DIHEDRALS CHANGE = 'OPTIMIZE'
WRITE_MODEL FILE = '1fas.ini2'