AMBER Archive (2003)

Subject: Re: AMBER question

From: Carlos Simmerling (carlos.simmerling_at_stonybrook.edu)
Date: Fri Jul 11 2003 - 10:24:30 CDT

I think what David is asking about is the distance between the atoms.
Marco's answer relates to the van der Waals term.
Carlos

----- Original Message -----
From: "Marco Aurelio Correia Preto" <mcpreto_at_fc.up.pt>
To: "David" <p9690409_at_dec4000.cc.ncku.edu.tw>;
<amber_at_heimdal.compchem.ucsf.edu>
Sent: Friday, July 11, 2003 10:29 AM
Subject: RE: AMBER question

> 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
>
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