AMBER Archive (2008)

Subject: Re: AMBER: Lennard-Jones parameters

From: Klenner_at_bioinformatik.uni-frankfurt.de
Date: Wed Feb 27 2008 - 16:11:50 CST

Hey,

I had pretty much the same problem, but this paper:

Artemenko N., Distance Dependent Scoring Function for Describing
Protein-Ligand Intermolecular Interactions.

explains how you can derive the Aij Bij Parameters given the well
depth and vdW radius for each atomtype.

This may help you as well, worked fine for me,

Cheers Alex

Quoting zhan chen <chenzha1_at_msu.edu>:

> Dear, all:
>
> I got a problem in finding out the lennard-Jones parameters in
> parm99. In parm94 or parm 99,there is one set of parameters
> including the inernuclear seperation of the ij pair and the potential
> well. I just don't know how can I calculate the A ,C value or sigma
> value for the lennard-jones formulas from these two parameters.
>
> ___ [ A C q1 q2 ]
> \ [ --- - --- + ----- ]
> /__ [ r^12 r^6 D r ]
> nonbonded
> pairs
>
> ___ [ sigma^12 sigma^6 q1 q2 ]
> \ [ ----- - --- + ----- ]
> /__ [ r^12 r^6 D r ]
> nonbonded
> pairs
>
> The answers will be useful for me to compute the solvation free
> enery with Amber parameter. Thank you in advance!
>
>
> Zhan

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