Re: [AMBER] I: help please

From: David A Case <>
Date: Fri, 18 May 2018 08:18:16 -0400

On Wed, May 16, 2018, giuseppe gatti wrote:
> I am an organic chemist, with a little experience of comp chem . Till now I
> worked with gaussian software and DFT model chem to compute activation
> barriers ( work published in Catalysis Science & Technology 7 (7), 1497-1507
> , <javascript:void(0)> Substituent and catalyst effects on GAC
> lactonization of γ-hydroxy esters)
> However, recently I computed strain energies from reactant to transition
> state by using the DIASM model of Hook and Bickelhaupt. Since I would like
> to rationalize these strain energies in terms of stretching , bending and
> torsion, for this purpose I need to know the key parameters, i.e. force
> constants.
> My idea is to input my DFT-optimized structure, say of a reactant, like
> 4-hydroxybutanoate
> to Antechamber and Leap and get the pmrtop file with the set of GAFF
> parameters which I need.
> Do You think that this procedure is reasonable and feasible? If Yes , how
> can be implemented in a batch of AMBER commands? I am a beginner of AMBER
> and so I need the help of an expert.

Your proposed calculations could be carried out, but I see some problems
with how you would interpret the results:

1. For a stable molecule (your reactant), the bond, angle and torsion
energies you would get (by using GAFF to construct the force field, and
then analyzing a DFT-optimized structure) would tell you more about
limitations in the force field than about strain energy in the molecule.
Arguably, a DFT-optimized structure has very little strain energy.

2. The proposed procedure would not seem to work at all for a
transition state, since we don't have ways of generating force field
models for these sort of species.

That said, you could certainly do the calculation and see if the results
led to any interesting insights. I'm no expert in this sort of thing,
so maybe others on the list have better insights.


AMBER mailing list
Received on Fri May 18 2018 - 05:30:04 PDT
Custom Search