AMBER Archive (2009)

Subject: Re: [AMBER] Regarding Urey-Bradley term in amber calculation

From: Jason Swails (
Date: Tue Nov 24 2009 - 06:48:31 CST

I would imagine you'd accomplish this by placing a "bond" between i and k.
You can then set the value of this bond force constant (which is a harmonic
interaction) in the frcmod when you load it into leap. You can use the
"bond" command in leap, just make sure that you have the appropriate
parameters available.

Good luck!

On Tue, Nov 24, 2009 at 1:48 AM, aneesh cna <> wrote:

> Dear amber users,
> I would like to keep "Urey-Bradley" term in angle potential form , in
> which
> takes the form of a harmonic interaction between the i-k sites of the
> covalently bonded triplet
> i-j-k (angle). How can I add angle distance term ( i-k distance) in Amber
> functional form for angle bending?. Waiting for your valuable reply
> Thanks in advance
> Aneesh
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list