AMBER Archive (2004)

Subject: Re: AMBER: question about force field

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Mon Jun 14 2004 - 11:14:18 CDT

each rotatable bond has multiple sets of 4 atoms
that can define the rotation. Think about ethane,
where the C-C bond can be defined by 9 sets of
4 atoms, each with the same middle 2 atoms
but different "outer" atoms (the hydrogens).
so, if you define a torsion term for the C-C,
it gets divided among the 9 "bond paths".
Carlos

----- Original Message -----
From: "scopio" <scopio_at_163.com>
To: <amber_at_scripps.edu>
Sent: Monday, June 14, 2004 11:05 AM
Subject: AMBER: question about force field

> Dear all:
>
> I am now reading a Cornell's paper titled with "A Second Generation
> Force Field for the simulation of Proteins, Nucleic Acids, and Organic
> Molecules", which descripes Cornell force field.
>
> I now have a question for torsinal parameters that what does the meaning
> of "Number of bond paths that the total Vn/2 is divided into". Could
> somebody give me hint? Thanks in advance!
>
> Best Regards!
>
> Liu
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