AMBER Archive (2008)

Subject: Re: AMBER: NON-BONDED parameters

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Mon May 05 2008 - 13:14:59 CDT

Hi Lin,

the non-bonded parameters are given (usually at the end) of the forcefield
parameter files that you are using. e.g. with ff99 you will find at the
end of parm99.dat entries like this one:

   OW 1.7683 0.1520 TIP3P water model

which tell you that the atom type OW (for a TIP3P water oxygen) has a
radius of 1.7683 A and a VDW well depth of 0.1520 kcal/mol.

You can modify these parameters by creating your own atom type and
specifying its non-bonded parameters in a frcmod file that you use to
build your system. Check the amber tutorial (number 3 or 4) for new
compounds on how to do that.

Regards,

Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA

On Mon, 5 May 2008, Chih-Ying Lin wrote:

>
>
> Hi
> where and how to print out / modify the NON-BONDED parameters ?
>
> Thanks
> Lin
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