AMBER Archive (2005)

Subject: Re: AMBER: Improper Torsional Parameters

From: David A. Case (case_at_scripps.edu)
Date: Thu Nov 03 2005 - 18:41:53 CST

On Wed, Nov 02, 2005, Ilyas Yildirim wrote:
>
> Anyways, is it proper to use the following improper torsional term in my
> frcmod?
>
> DH-DH-O -C 1.1 180. 2. [Dummy Params]
>
> (if I want to make use of "X -X -N2-H 1.0 180. 2.)

Of course, "dummy" parameters shouldn't really make a difference (since you
will always need to have a thermodynamic cycle in which their effects cancel
when taking the differences along two sides.

However, we generally make the internal dummy parameters the same as those
for the real atoms the are replacing. So I would tend to suggest:

DH-DH-O -C 1.0 180. 2. [Dummy Params]

for your example above.

...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu