Re: [AMBER] Dihedral restraint on a C=N double bond

From: Carlos Simmerling <>
Date: Thu, 30 Dec 2021 16:30:15 -0500

r1, r2, r3 and r4 correspond to the angles where the restraint function
changes. They can't alll be the same like in your example, you will need to
edit them. Check the manual for details on what each means and the units.

On Thu, Dec 30, 2021, 3:12 PM Liao <> wrote:

> Dear Amber community,
> I’m struggling to properly restrain the cis-tran geometry of a hydrazone
> (R1R2C=NNH2) as part of my small molecule ligand. The double bond should be
> planar and not freely rotatable, however gaff2 doesn’t seem to model this
> properly (or my setup is wrong somewhere but I haven’t detected such yet),
> and when I start with a cis, the dihedral involving the double bond will
> rotate and turn to trans and favor trans. The frcmod file I looked into,
> there is a line on the dihedral section describing this dihedral,
> "ca-ce-n2-ns 2 1.600 180.000 2.000 same as X
> -ce-ne-X , penalty score=160.5"
> though changing 180 to 0 didn’t make a difference. Not completely sure
> what the other numbers mean.
> Anyway, I moved on and decided to use dihedral restraints in the
> simulation, but that also doesn’t seem to be making an effect. It’s
> rotating pretty freely. Here’s the restraint file generated by cpptraj for
> that dihedral:
> &rst iat=1152,1155,1156,1157,0
> r1=1, r2=1, r3=1, r4=1, rk2=64.000000, rk3=64.000000,
> nstep1=0, nstep2=0,
> &end
> I confirmed the numbers 1152,1155,1156,1157 correspond to the correct 4
> atoms of C, C, N, N. The restraint weight was gradually increased from 10
> to 64, which is should be high enough I believe.
> What could be wrong here?
> Thank you and appreciate any help.
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Received on Thu Dec 30 2021 - 14:00:03 PST
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