AMBER Archive (2009)

Subject: Re: [AMBER] GAFF parameter

From: Jason Swails (jason.swails_at_gmail.com)
Date: Tue Oct 20 2009 - 09:57:09 CDT

Stefano,
ho atom types in gaff are given a zero van der waals. This is not a
mistake, but rather on purpose. If you check, the atom will still have a
charge, so all non-bonded terms from that atom will be electrostatic in
nature. I believe that FF99 shares the same trait in that H atoms bonded to
O have no VDW radii.

All the best,
Jason

On Tue, Oct 20, 2009 at 9:26 AM, stefano_elli_at_libero.it <
stefano_elli_at_libero.it> wrote:

> Hello
>
> I would like to ask a question on NON Bond parameter of GAFF and on AMBER
> force field.
>
> I have not a clear idea on how no bond vdw parameter work.
>
> For example in the "gaff.dat" file at the bottom there are four column that
> begin with:
>
>
> MOD4 RE
>
> h1 1.3870 0.0157 Veenstra et al JCC,8,(1992),963
> h2 1.2870 0.0157 Veenstra et al JCC,8,(1992),963
> ho 0.0000 0.0000
> ...
> END
>
> 1) How is the right mening of these parameter?
>
> 2) Why the atomtype 'ho' has both zero parameters?
>
> Thank you so much!
>
> Stefano
>
>
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> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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