AMBER Archive (2001)

Subject: 1-4 nonbonded interactions

From: David L. Bostick (dbostick_at_physics.unc.edu)
Date: Wed Apr 18 2001 - 13:37:12 CDT

Hello,

I have a system consisting of a dppc bilayer and protein embedded within.
The model for the each dppc lipid molecule requires that the headgroup 1-4
electrostatic interactions be divided by 2.0 and the van der Waals
interactions be divided by 8.0. The potential in the tails employs a sum
of dihedrals that is equivalent to the Ryckaert-Bellemans potential for
butane and therefore requires no such screening of nonbonded interactions.
I am employing the amber98 forcefield for the protein which will require
standard screening (default values for SCEE and SCNB). However, there is a
prosthetic group on one of the residues that I incorporated into the
protein in amber as a nonstandard residue. The model for this prosthetic
group that I wish to use requires that there is no screening of nonbonded
interactions.

This seems to present a dilemma in amber, because there is only an option
to change SCEE and SCNB uniformly for a system. Is there some way of which
I am unaware that would allow me to do 1-4 nonbonded interaction screening
in different ways for different parts of different molecules in the system?

Thank you in advance,
David

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David Bostick Office: 262 Venable Hall
Dept. of Physics and Astronomy Phone: (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall dbostick_at_physics.unc.edu
Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
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