Generate Amber-style distance/angle/torsion restraints

rst <mask1> <mask2> [<mask3>] [<mask4>] r1 <r1> r2 <r2> r3 <r3> r4 <r4> rk2 <rk2> rk3 <rk3> {[parm <parmfile / tag> | parmindex <#>]}[{ref <refname> | refindex <#> | reference} [offset <off>] [width <width>]] [out <outfile>]

<mask1> (Required) First atom mask.
<mask2> (Required) Second atom mask. If only two masks assume distance restraint.
[<mask3>] (Optional) Third atom mask. If 3 atom masks assume angle restraint.
[<mask4>] (Optional) Fourth atom mask. If 4 atom masks assume dihedral restraint.
rX <rX> Value of RX (X=1-4, default 0.0)
rk2 <rk2> Value of RK2 (force constant to be applied when R is R1 <= R < R2)
rk3 <rk3> Value of RK3 (force constant to be applied when R is R3 <= R < R4)
[parm <parmfile / tag> | parmindex <#>] Topology to be used for atom masks.
{ref <refname> | refindex <#> | reference} Use distance/angle/dihedral in reference structure to determine values for r1, r2, r3, and r4. The value of r2 is set to <r2> + <off>, r3 = r2, r1 = r2 – <width>, r4 = r3 + <width>.
[offset <off>] (Reference only) Value to offset distance/angle/torsion in reference by (default 0.0).
[width <width>] (Reference only) Width between r1 and r2, r3 and r4 (default 0.5).
[out <outfile>] Write restraints to outfile. If not specified, write to STDOUT.

Generate Amber-style distance restraints for use with nmropt=1. This is particularly useful for generating distance restraints based off of reference coordinates. For example to generate a distance restraint between two C5’ atoms using the current distance between them in a reference structure, offsetting the distance by 1.0 Ang.:

parm 30bp-longbox-tip3p-na.parm7
reference 30bp-longbox.rst7
rst :1@C5’ :31@C5’ reference offset 1.0 rk2 10.0 rk3 10.0 out output