RE: AMBER question

From: Marco Aurelio Correia Preto <>
Date: Fri, 11 Jul 2003 15:29:11 +0100

Hi David:

In relation to Rij, I think I can help you a litle:

Rij = Rii + Rjj (and Rii and Rjj is half the equilibrium distance between two equal atoms - I think some times it's refered to as van Der Walls radius).
rij in the electrostatic energy potencial it will be the distance between the atom i and j!

Point charges are part of the parameterization of the f.f.! If you are working with non paremeterized a.a residues, you'll have to get point charges from Merz - Kollman method using some quantum mechanics packadge (I think that the a. a. parameterization on Amber was performed at HF/6-31G* level)

Anyone correct me if I'm wrong!

Hope it helps

Marco Preto
PH.D student
FCUP - Protugal

-----Original Message-----
From: David []
Sent: Fri 7/11/2003 2:42 PM
Subject: AMBER question

Dear AMBER reflector:

Hello, I am a graduate student from Taiwan. I sent AMBER question before.

When I calculate amino acid residue, I have AMBER force field questions as

1. In AMBER electrostatic energy term, how to get the value of dielectric
constant and point charges ?

2. How to define the Rij in electristatic energy term, and how to get its
value ?

Wish you can give me some suggestions. Be very grateful to you!

Best Regards.

Received on Fri Jul 11 2003 - 15:53:00 PDT
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