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restraints.txt
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A restraints file consists of two sections. The sections are separated by an empty line.
Lines starting with # are always skipped
1. Selection section: <selection identifier> <number of atoms in selection> <n1> <n2> ... where <nX> is the atom number among all the numbers in the system.
Example: a receptor with 3000 atoms and a ligand with 1000 atoms:
sel 3 293 294 3008
selection "sel" consists of atoms 293 and 294 of the receptor and atom 8 of the ligand.
2. Restraints section: <selection identifier 1> <selection identifier 2> <restraint type> [parameters]
restraint types:
1: harmonic maximum distance restraint: <maximum distance> <force constant>
force increases linearly with the violation
2: HADDOCK maximum distance restraint: <maximum distance> <force constant>
<max violation> <chance of random removal>
force increases linearly with the violation
force cannot be bigger than force at max violation:
i.e.: harmonic up to max violation, linear afterward
3: harmonic minimum distance restraint: <minimum distance> <force constant>
force increases linearly with the violation
4: harmonic distance restraint: <equilibrium distance> <force constant>
force increases linearly with the violation
used for bond and angle restraints in flexible interface simulations
5: double quadratic minimum distance restraint: <minimum distance> <force constant>
used for steric repulsion in flexible interface simulations
6: step potential, use only for scoring!
7: positional restraint: <minimum distance> <maximum distance> <force constant>
<type> <refex> <refey> <refez> See below for explanation of type etc
8: bump restraints: <minimum distance> <maximum distance> <slope> <force constant>
double quadratic potential with flat potential between minimum distance and maximum distance
slope below minimum distance and above maximum distance. Goes smoothly to zero at
minimum distance-slope and maximum distance-slope. Slope and force constant determine the
height of the potential well/bump. Attractive for negative force constant.
The "chance of random removal" indicates the chance that a restraint is not used at all.
This is determined by a random number generated from a structure's seed. Therefore, the same seed with the same restraint file causes the same restraints to be enabled or disabled within every docking stage.
Orthogonality issue: the seed number is also used in pure MC mode.
************************
Examples:
(start of file)
Ile54_CA 1 385
Leu1001_CA 1 2356
Ile54_CA Leu1001_CA 1 2.4 2
(end of file)
Defines a harmonic restraint between atom 385 and atom 2356. The maximum distance is 2.4 A: this distance or less gives no energy penalty/force.
At 3.4 A, the atoms experience an attractive force of 2 kcal/mol / A, and the energy penalty is 1 kcal/mol
At 5.4 A, the atoms experience an attractive force of 18 kcal/mol / A, and the energy penalty is 9 kcal/mol.
(start of file)
Gly31 4 31 32 34 35
Ser281 6 1064 1065 1066 1067 1068 1069
Gly31 Ser281 2 2.0 1.0 1.0 0.6
(end of file)
Defines a HADDOCK restraint between a selection of 4 atoms and a selection of 6 atoms. The maximum effective distance is 2.0 A: this distance or less gives no energy penalty/force. The effective distance is (sum(distances**-6))**-1/6.
The restraint is harmonic between 2.0 and 3.0 A and then becomes linear (the force constant doesn't increase further beyond 3.0 A).
At 2.5 A, the atoms experience an attractive force of 1 kcal/mol / A, and the energy penalty is 0.5 kcal/mol.
At 3.0 A, the atoms experience an attractive force of 2 kcal/mol / A, and the energy penalty is 1 kcal/mol.
At 4.0 A, the atoms experience an attractive force of 2 kcal/mol / A, and the energy penalty is 3 kcal/mol.
The restraint has a 60 % chance not to be in effect at all.
**************
Tbl Format examples
*****************
Restraints can also be specified with the tbl syntax and converted to ATTRACT restraint format with tools/tbl2attract.py
1. Harmonic restraints
assign <selection1>
<selection2>
<distance> <dmin> <dmax>
assign (segid A and resid 4 and name CA)
(segid B and resid 12 and name CA)
10.0 10.0 0.0
Use tbl2attract.py with --mode harmonic to define a maximum distance restraint of distance+dmax=10.0+0.0=10.0 A between the receptor protein's residue number 4 CA atom
and the ligand protein's residue number 12 and CA atom. A mininum distance restraint would be defined for distance-dmin if that distance is larger than 0.
2. Positional restraints
Attract can also be given a restraints file in which for chosen residues of a ligand maximum and/or minimum coordinates can be defined.
Only those docking results which fullfill these area restraints get a good scoring and thus are part of the top results.
format:
for each group of residues a new restraints selection can be defined: assign <selection> <distance> <dmin> <dmax> <type> <refe-x> <refe-y> <refe-z>
<selection> is built like this:
assign (
( name CA and resid #1 and segid B)
or ( name CA and resid #2 and segid B)
or ( name CA and resid #3 and segid B)
or ( name CA and resid #4 and segid B)
.
.
.
or ( name CA and resid #N and segid B)
)
That means that Attract will make sure that the C-Alpha atom (CA) of the resid #N in the ligand (segid B) will fullfill the given restraints.
<distance>: distance from the reference point
<dmin> <dmax>: minimum and maximum distance relating to the coordinates defined by <distance>.
<type> can be: x, y, z, xy, xz, yz or xyz
The type determines which coordinate(s) of the atom are used to compute <distance>
e.g. "x" defines a planar region, "xy" a cylindrical region and "xyz" a spherical region
<refe-x> <refe-y> <refe-z>: defines the reference point
!!!Important!!!
tbl2attract.py cannot handle the case if <distance> and <dmax> are both zero. So if no maximum distance restraint is required and <distance> is equal zero,
a large value for <dmax> should be given, like 1000.
examples:
assign (
( name CA and resid 501 and segid B)
or ( name CA and resid 656 and segid B)
or ( name CA and resid 676 and segid B)
) 0.0 0.0 10 xy 8 30 0
assign (
( name CA and resid 501 and segid B)
or ( name CA and resid 676 and segid B)
) 0.0 0.0 7 z 0 0 100
assign ( ( name CA and resid 656 and segid B)) 0.0 0.0 0.1 z 0 0 130
assign (
( name CA and resid 21 and segid B)
or ( name CA and resid 22 and segid B)
) 0.0