Assign distance restraints:
If you know what atom pairs should be in contact or in some distances,
you can use this option to upload a
text file including contact and/or distance
information of atom pairs.
This file can specify the atom-based distances
between ith and jth residues
in the format:
Res_No.j Atom_type_j Distance_in_Angstroms Weight Restraint Function"
12 CB 50 CB 8.1 1.0 HARMONIC
14 CB 57 CA 6.2 2.0 HARMONIC
21 CB 43 CA 4.0 0.5 RECIPROCAL
124 CA 84 CB 17.4 10.0 RECIPROCAL
36 CB 120 CB 17.4 0.25 HARMONIC
The first and third positions in the file specify the residue indices for residue i and j, respectively, while the second and fourth positions specify the atom types
from residues i and j, respectively, to enforce the distance restraint for. Here,
distance restraints may be enforced between CA or CB atoms. The fifth position specifies the distance between the two atoms and the sixth position specifies the weight to apply to the restraint. The final position specifies the function that will be used to enforce the distance, either a harmonic restraint or a reciprocal squared restraint.
Note, harmonic restraints will invoke a heavy penalty if the restraints are not satisfied, while the reciprocal squared function is less severe. If many distances are specified, it may be better to use the reciprocal squared function, while if only a handful of restraints are specified, it may be better to use harmonic restraints.
The weight for each constraint can be set to increase the likilihood that it will be satisfied.
If they are not specified, the weights will automatically be set to 1 by FoldDesign.
is an example of the restaint file.