Hi,
On Mon, May 11, 2026 at 6:40 AM Manasa Bharath ic44158 via AMBER
<amber.ambermd.org> wrote:
> I also want to confirm the unit of force/force constant used for rk2 and rk3.
> Is it in *kcal mol⁻¹ Å⁻²*, as used in AMBER NMR-style restraints?
Cpptraj is just generating input for sander, so the force constants
will automatically be in the units sander uses.
>
> Any guidance or examples for DNA systems would be very helpful.
Here's some input that will generate a restraint between atom O2 of a
C base and N2 of a G base in two different ways. The first uses r2=r3
distance calculated from an input reference, and the second has all
r1-r4 values specified.
parm adh026.3.pdb
reference adh026.3.pdb
set RK2 = 5
set RK3 = $RK2
# Use r2=r3 distance from the reference
rst :6.O2 :11.N2 reference offset 0.5 out temp.restraints.dat rk2 $RK2 rk3 $RK3
# Specify all distances
rst :6.O2 :11.N2 r1 2.8 r2 3.0 r3 3.0 r4 3.2 out temp.restraints.dat
rk2 $RK2 rk3 $RK3
You'll have to adapt this for your own needs and whatever bases you
have in your structure. Hope this helps,
-Dan
>
> Regards,
> Manasa
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Received on Wed May 13 2026 - 10:30:07 PDT
