AMBER Archive (2008)

Subject: Re: AMBER: NON-BONDED parameters

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Mon May 05 2008 - 17:10:05 CDT

HI
For aromatic systems 1-4 nonbonded interactions are excluded .
Did AMber appliy this rule also to 1-4 interactions involving the nitrogen atoms?

Thanks
Lin

----- Original Message -----
From: Thomas Steinbrecher <steinbrt_at_scripps.edu>
Date: Monday, May 5, 2008 11:20 am
Subject: Re: AMBER: NON-BONDED parameters
To: amber_at_scripps.edu

> 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
> > ------------------------------------------------------------------
> -----
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
> --------------------------------------------------------------------
> ---
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu