[AMBER] Torsional profile of butane

From: Yingjie Wang <wang1710.umn.edu>
Date: Thu, 26 Jun 2014 12:57:32 -0500

Hi AMBER experts,

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

Application of RESP charges to calculate conformational energies, hydrogen
bond energies, and free energies of solvation,
Wendy D. Cornell
 , Piotr Cieplak
 , Christopher I. Bayly
 , Peter A. Kollmann
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?

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

CT-CT-CT-CT 1 0.18 0.0 -3. Junmei et al,
CT-CT-CT-CT 1 0.25 180.0 -2. Junmei et al,
CT-CT-CT-CT 1 0.20 180.0 1. Junmei et al,

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?

Thank you very much. I fully appreciate your help.



Yingjie Wang
Ph.D candidate for chemical physics
Prof. Gao research group
University of Minnesota at Twin Cities
Room 63, Kolthoff Hall
207 Pleasant St. SE
Minneapolis, MN 55455
Cell: (612)-860-1634
Office: (612)-625-5325
Email:wang1710.umn.edu <lsjyppku.gmail.com>
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Received on Thu Jun 26 2014 - 11:00:02 PDT
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