Then it’s much simpler to use a harmonic potential, bond type 6. This will also work with intermolecular interactions.
Hess hi,
is this correct:
; restraints for angles
[ intermolecular_interactions ]
[ angle_restraints ]
;i j k l type theta fc multiplicity
1608 1610 4651 4645 1 180.0 2000 1
is this correct format; i want to restrain 1610 4651 4645 at 180 degrees.
That looks ok. But you only mention three atoms in the last sentence.
My distance restraint file is (disres.itp), the content pasted below:
[ distance_restraints ]
; ai aj type r0 r1 r2 weight
; Example:
2 18 1 0.3 0.299 0.301 1000.0 ; Restrain atoms 10 and 20 to be between 0.3 and 0.3 nm, with r0 = 0.3 nm
The error message I am getting is:
ERROR 1 [file disres.itp, line 4]:
Atom index (2) in distance_restraints out of bounds (1-1).
This probably means that you have inserted topology section
“distance_restraints”
in a part belonging to a different molecule than you intended to.
In that case move the “distance_restraints” section to the right molecule.
I am attaching the current simple mdp file for minimization.
Can you please help me figure out the correct way to undertake the distance restraints between two atoms which are not covalently connected?
The error message probably tells you exactly what the issue is. My guess is that you put/included these restraints somewhere at the end of your topology and now they are acting on an (I guess) ion. You need to put/include this in the moleculetype section of your protein.
It also looks like you misinterpreted how the restraint works. The values 0.299 and 0.301 are not bounds for the distance, but for the harmonic potential. After these the potential becomes linear, so the restraint is extremely weak.
Furthermore, I think that you could use a simple harmonic potential: bonds type 6.