AMBER Archive (2005)

Subject: RE: AMBER: intramolecular nonbonded interactions in AMBER force field

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Apr 20 2005 - 17:33:41 CDT

Yes they are.

Generally 1-2 and 1-3 terms do not include VDW or electrostatics as these
effects are included in the bond and angle parameterisation. 1-4 VDW and
electrostatic interactions are generally scaled by 1.2. All other VDW and
electrostatic interactions, both intra molecular and inter molecular are
calculated without scaling as long as the distance between the atom pairs is
less than the nonbonded cutoff (default = 8 angstroms).

I hope this helps
All the best
Ross

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of John Silvio Vieceli
> Sent: 20 April 2005 15:07
> To: amber_at_scripps.edu
> Subject: AMBER: intramolecular nonbonded interactions in
> AMBER force field
>
> Hi,
>
> Are intramolecular nonbonded interactions applied to atoms
> separated by
> more than three bonds in the AMBER force field? I understand that 1,4
> LJ and Coulomb interactions are calculated and scaled by 1/2
> and 1/1.2,
> respectively. But what about 1,5 and beyond? Are these interactions
> included and, if so, scaled by any factor? Thank you.
>
> --
> John S. Vieceli, Ph.D.
> Zymeworks, Inc.
> 201-1401 West Broadway Avenue
> Vancouver, B.C. V6H 1H6
> (604) 678-1388 ext. 25
> john_at_zymeworks.com
> www.zymeworks.com
>
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