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MAKE_RESTRAINTS -- make restraints

RESTRAINT_TYPE = <string:1> 'STEREO' restraint type to be calculated: 'STEREO' | 'BOND' | 'ANGLE' | 'IMPROPER' | 'DIHEDRAL' | 'MRFP_STEREO' | 'MRFP_BOND' | 'MRFP_ANGLE' | 'MRFP_DIHEDRAL' | 'SPHERE' | 'SPHERE14' | 'LJ' | 'LJ14' | 'COULOMB' | 'COULOMB14' | 'ALPHA' | 'STRAND' | 'SHEET' | 'DISTANCE' | 'USER_DISTANCE' | 'NONB_PAIR_SPLINE' | 'PHI-PSI_BINORMAL' | 'PHI-PSI_CLASS' | 'PHI_DIHEDRAL' | 'PSI_DIHEDRAL' | 'OMEGA_DIHEDRAL' | 'CHI1_DIHEDRAL' | 'CHI2_DIHEDRAL' | 'CHI3_DIHEDRAL' | 'CHI4_DIHEDRAL'
RADII_FACTOR = <real:1> 0.82 factor for van der Waals radii
TOPOLOGY_MODEL = <integer:1> 3 selects topology library: 1-10
DIH_LIB_ONLY = <logical:1> off whether to use only library, not homologs for dihedral angle rsrs
MNCH_LIB = <integer:1> 1 which MNCH lib to use in MAKE_RESTRAINTS
INTERSEGMENT = <logical:1> on whether to restrain inter-segment non-bonded pairs
ADD_RESTRAINTS = <logical:1> off whether to add new restraints to existing restraints
RESIDUE_GROUPING = <integer:1> 1
MAXIMAL_DISTANCE = <real:1> 999 maximal distance for distance restraints
RESIDUE_SPAN_RANGE = <integer:2> 0 99999 range of residues spanning the allowed distances; for MAKE_RESTRAINTS, PICK_RESTRAINTS, non-bonded dynamic pairs
RESIDUE_SPAN_SIGN = <logical:1> on whether to do N*(N-1)/2 loop for atom pairs in MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance'
RESTRAINT_SEL_ATOMS = <integer:1> 1 a restraint other than non-bonded pair has to have at least as many selected atoms
NONBONDED_SEL_ATOMS = <integer:1> 1 a non-bonded pair has to have at least as many selected atoms
EXCL_LOCAL = <logical:4> on on on on whether to exclude bonds, angles, dihedrals, explicit excl pairs from the homology-derived distance rsrs
ACCESSIBILITY_TYPE = <integer:1> 8 type of solvent accessibility: 1-10
DISTANCE_RSR_MODEL = <integer:1> 1 the model for calculating distance restraints: 1-7
RESTRAINT_STDEV = <real:2> 0.0 1.0 transforming factors for standard deviations (y=a+bx) in models 1-6 or standard deviation for model 7 (a)
RESTRAINT_STDEV2 = <real:3> 0 0 0 transforming standard deviation in models 3-6: S' = S + [ a + b max(0, c-g) ]
RESTRAINT_PARAMETERS = <real:0> 3 1 3 3 4 2 0 0.0 0.087 restraint parameters for 'USER_DISTANCE'
ATOM_FILES_DIRECTORY = <string:1> './' input atom files directory list (e.g., 'dir1:dir2:dir3:./:/')
BASIS_PDF_WEIGHT = <string:1> 'LOCAL' a method for calculation of basis pdf weights: 'LOCAL' | 'GLOBAL'
BASIS_RELATIVE_WEIGHT = <real:1> 0.05 the cutoff weight of basis pdf's for their removal
RESIDUE_IDS = <string:0> '' residue id (number:chnid)
SPLINE_ON_SITE = <logical:1> off whether to convert restraints to splines
SHEET_H-BONDS = <integer:1> 7 specify hydrogen bonds in a beta-sheet

Requirements:
topology & parameters [& alignment] [& picked atoms sets 2 and 3]

Description:
This command calculates and selects new restraints of a specified type. See the original papers for the most detailed definition and description of the restraints [Šali & Blundell, 1993,Šali & Overington, 1994]. The calculation of restraints of all types is now (partly) limited to the selected atoms only (either set 1, or 2 and 3; see below).

If ADD_RESTRAINTS is off, all old restraints are deleted, otherwise new restraints are added to the old ones.

RESTRAINT_TYPE selects the types of the generated restraints. Only one restraint type can be selected at a time, except for the stereochemical restraints (BOND, ANGLE, DIHEDRAL, IMPROPER) that can all be calculated at the same time. It is useful to distinguish between the stereochemical restraints and homology-derived restraints. The stereochemical restraints are obtained from libraries that depend on atom and/or residue types only (e.g., CHARMM 22 force field [MacKerell et al., 1998] or statistical potentials), and do not require an alignment with template structures. In contrast, the homology-derived restraints are calculated from related protein structures, which correspond to all but the last sequence in the alignment (the target). These templates are read from coordinate files, which are the only data files required. All restraints are added to the existing restraints, even if they duplicate them (but see the comment for the 'OMEGA' restraints below).

Stereochemical restraints:

Homology-derived restraints:

BASIS_RELATIVE_WEIGHT is the cutoff for removing weak basis pdf's from poly-Gaussian feature pdf's: a basis pdf whose weight is less than the BASIS_RELATIVE_WEIGHT fraction of the largest weight is deleted.

Example:


# Example for: MAKE_RESTRAINTS, SPLINE_RESTRAINTS, WRITE_RESTRAINTS

# This will compare energies of bond length restraints expressed
# by harmonic potential and by cubic spline.

SET OUTPUT_CONTROL = 1 1 1 1 1

READ_TOPOLOGY   FILE = '$(LIB)/top_heav.lib'
READ_PARAMETERS FILE = '$(LIB)/par.lib'
READ_MODEL FILE = '1fas', MODEL_SEGMENT = '1:' '61:'
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'
TRANSFER_XYZ
BUILD_MODEL INITIALIZE_XYZ = off
WRITE_MODEL FILE '1fas.ini'

MAKE_RESTRAINTS RESTRAINT_TYPE = 'bond'
WRITE_RESTRAINTS FILE = '1fas-1.rsr'
ENERGY DYNAMIC_SPHERE = off

SPLINE_RESTRAINTS SPLINE_RANGE = 5.0, SPLINE_DX = 0.005, SPLINE_SELECT = 3 1 1
CONDENSE_RESTRAINTS
WRITE_RESTRAINTS FILE = '1fas-2.rsr'
ENERGY


next up previous contents index
Next: DEFINE_SYMMETRY define Up: Calculation of spatial restraints Previous: Specification of pseudo atoms   Contents   Index
Ben Webb 2004-10-04