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

From: Liao <>
Date: Thu, 30 Dec 2021 19:55:31 -0600

Thanks there Carlos,

Changing the r1-r4 values finally made it work, looks like there had to be a large enough distance between r1 and r2 (and r3 and r4). I had changed it to all 1s after the direct output from cpptraj giving a distance of 0.5 between r1 and r2 didn’t work. Now the distance between r1 and r2 is 30, the restraint is working pretty OK at 10kcal/mol/A.

> On Dec 30, 2021, at 3:30 PM, Carlos Simmerling <> wrote:
> 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 - 18:00:02 PST
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