AMBER Archive (2003)

Subject: RE: AMBER question

From: Marco Aurelio Correia Preto (mcpreto_at_fc.up.pt)
Date: Fri Jul 11 2003 - 09:29:11 CDT

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 [mailto:p9690409_at_dec4000.cc.ncku.edu.tw]
Sent: Fri 7/11/2003 2:42 PM
To: amber_at_heimdal.compchem.ucsf.edu
Cc:
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
below:

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.

David