Re: [AMBER] Torsion parameters

From: Karl Kirschner <>
Date: Fri, 28 Jan 2022 13:59:23 +0100

Hello Cenk,

  In our parameterization work, we perform constraint optimization In
vacuum (i.e. gas-phase) conditions. In the molecular mechanics constraint
optimization, we allow everything to relax around the constraint that we
specified, which matches the gas-phase constraint optimization that was
done using QM (or DFT). Then, when possible, we validate the resulting
parameters for usage in solution conditions.

The following is an example from my files that I could find quickly, which
will start you down a possible path.

* <>*:
Constraint Minimization
    imin=1, dielc=1,ntb=0,
   &wt type='END' &end

 &rst iat = 14, 11, 8, 5,
          r1 = 59.0, r2 = 60.0, r3 = 60.0, r4 = 61.0,
          rk2 = 30000.0, rk3 = 30000.0,

Of course, there are other approaches like you mention. For example, if you
computed relative QM energies using implicit solvent, then one might
consider doing the MM optimization similarly. I hope this helps.


On Fri, Jan 28, 2022 at 1:30 PM Cenk Andac <> wrote:

> Dear Amber community,
> I have been currently developing amber parameters for a small molecule.
> Rather than using GAFF, i would like to develop parameters using an AMBER
> ff.
> I have already determined resp charges , bond and angle parameters for the
> small molecule. I have also plotted a potential energy curve determined at
> the quantum computations level. I now need to optimize my potential curve
> by comparing it to non- bonded potentials determined by MM. I used to know
> the procedure back in 2007 and I had saved my sander input parameters for
> that in my old hard disk. Unfortunately , my hard disk is unreachable and
> useless now. I don't have the sander input parameters on top of my head.
> Thus, I kind a got stuck here. My question is I just can't remember if I am
> supposed to do one-step energy computations for increasing steps of the
> torsions under vacuum or in GB implicit solvent MD conditions.
> I ll appreciate it much if an amber expert out there could drop the
> required sander parameters here.
> Best.
> Cenk Andac
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Fri Jan 28 2022 - 05:30:02 PST
Custom Search