Re: [AMBER] Torsional profile of butane

From: FyD <>
Date: Fri, 27 Jun 2014 07:55:02 +0200

Dear Yingjie,

> As a new learner to AMBER, I just want to study a simple case: the
> torsional profile of along the C2-C3 bond of n-butane from 0 to 360
> degrees. I am developing QM/MM methods in Gaussian program where AMBER is
> an available choice for MM part, but the AMBER96 parameter used in Gaussian
> doesn't specify the partial charges nor the full Fourier terms of butane.
> The first question is on the RESP charges. As I found in the following
> literature,
> Application of RESP charges to calculate conformational energies, hydrogen
> bond energies, and free energies of solvation,
> Wendy D. Cornell
> J. Am. Chem. Soc., 1993, 115 (21), pp 9620?9631
> Different RESP charges are assigned to gauche and trans conformation of
> butane. Does it mean that we cannot scan the whole potential profile from 0
> to 360 degree with the same set of charges? If we can, what vaules should
> we use?

You could use R.E.D. Server Dev. which interfaces PyRED to perform:
  - charge derivation involving multiple orientations & multiple conformations
  - atom typing: GAFF is - for sure - not required here
  - force field parameter generation
  - LEaP script generation
Using the frcmod file generated by PyRED you can directly set the
target (see below) dihedral force field parameters to zero to be able
to fit them to the QM profile...

Concerning MEP-based charge derivation and important article to read
here is (at least to be aware of an important limitation):
   See the RRMS value of the charge fitting step; for instance:

> The second questions is on the Fourier components of the C-C-C-C bond. Are
> the following third components from PARM99.dat are what we want to use
> exactly?
> CT-CT-CT-CT 1 0.18 0.0 -3. Junmei et al, 1999
> CT-CT-CT-CT 1 0.25 180.0 -2. Junmei et al, 1999
> CT-CT-CT-CT 1 0.20 180.0 1. Junmei et al, 1999
> The third question is on the full MM torsional profile of butane using the
> AMBER program. If I have the correct parameter from the first two
> questions, I might be able to get the profile just using Gaussian, but it
> would be ideal to have referenced results from the AMBER program. As I am
> new to AMBER and has no idea on the detailed specification, can anyone give
> some suggestions or even example inputs on such kind of calculation?

In Butane 9 paths are found; i.e. the following specific dihedrals:

So you might want also to look at Ethane for HC-CT-CT-HC, and then at
Propane for HC-CT-CT-CT.

regards, Francois

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Received on Fri Jun 27 2014 - 02:00:02 PDT
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