Re: [AMBER] Torsional profile of butane

From: Yingjie Wang <wang1710.umn.edu>
Date: Fri, 27 Jun 2014 09:38:41 -0500

Jason and Francois,

Thank you for your help. I will carefully examine your suggestions and try
to find the best way to solve my problem.

Best,

Yingjie


On Fri, Jun 27, 2014 at 12:55 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:

> 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
> http://q4md-forcefieldtools.org/REDServer-Development/ 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):
> http://onlinelibrary.wiley.com/doi/10.1002/jcc.540150705/abstract
> See the RRMS value of the charge fitting step; for instance:
> http://q4md-forcefieldtools.org/REDDB/projects/W-43/
>
> > 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:
> 1 CT-CT-CT-CT + 4 HC-CT-CT-HC + 4 HC-CT-CT-CT
>
> 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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>



-- 
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´╝Üwang1710.umn.edu <lsjyppku.gmail.com>
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Received on Fri Jun 27 2014 - 08:00:03 PDT
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