Re: [AMBER] AMBER VS QM energy calculations for dihedrals

From: Ilyas Yildirim <>
Date: Wed, 28 Apr 2010 10:32:42 -0400 (EDT)

On Wed, 28 Apr 2010, Palermo Giulia wrote:

> Dear all,
> I am checking the energies of amber force field (gaff, parametrized with antechamber and resp charges)
> of a ligand for the rigid rotation around a torsion
> against HF/DFT energies. My aim is to perform a conformational sampling by means of straigtforward MD.
> The complex is a piperidine 1-caboxylic acid phenylamine that is something like
> h h1
> c-c o1
> / \ ||
> h-c c-c - n-......
> \ / h
> c-c
> h h
> When I rigidly (no minimization upon torsion change) rotate the torsion around the Npiperidine - Ccarbonilic - NH - Caromatic dihedral angle
> (atom type: n-c-n-ca) I found that, when h1(type 'ha' in gaff) is less than 1.59 angstrom from o1 (type 'o' in gaff ) I obtain a very high energy for the
> force field (around 150 kcal/mol) mostly due to wdV terms (calculated by doing a single step in sander). In HF and various DFT for the same configuration
> I do not obtain this peak (the barrier for the rotation stays around 6/7 kcal). If I carry out a non rigid torsion scan this effect is not

Most probably in the QM calculation, the structure is first optimized and
then the energy is calculated. Otherwise, for a distance of 1.59 A, you
will get a huge energy. So, a rigid rotation without a minimization cannot
be direcly compared to QM results. I do not think that this is worrisome.
If the barrier was that high even after minimization, that would be

There are different approaches on how to do the torsional potential energy
surface scan. We did PES scan for ribonucleosides where we restrained
most of the dihedrals in the QM and MM calculations. You can take a look
at the following paper to see the computational methodology.

"Reparameterization of RNA CHI Torsion Parameters for the AMBER Force
Field and Comparison to NMR Spectra for Cytidine and Uridine", Ilyas
Yildirim, Harry A. Stern, Scott D. Kennedy, Jason D. Tubbs and
Douglas H. Turner, JCTC, 2010

Best regards

Ilyas Yildirim

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Received on Wed Apr 28 2010 - 08:00:03 PDT
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