RE: AMBER: double counting of potentials

From: Ross Walker <>
Date: Tue, 31 May 2005 16:21:43 -0700

Hi Julie,

> Is there any double counting of potentials with respect to
> 1-4VDW and 1-3
> bending
> and the non-bonded rotational barriers? How does AMBER handle this?

1-2 and 1-3 interactions are skipped (in the code) when doing the non-bonded
interactions since the bond and angle terms are parameterised with this in
mind. I.e. they include the VDW and EEL in the force constants as it were.

1-4 interactions (dihedrals) are calculated using the dihedral term but VDW
and EEL terms are also calculated here. Although these are scaled by 1.2.
The dihedral barrier heights etc were fitted within this scaling regime and
so this scaling avoids 'overcounting' the contribution here.

I hope this makes sense.
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Wed Jun 01 2005 - 00:53:00 PDT
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