AMBER Archive (2009)

Subject: Re: [AMBER] Question about improper torsions...

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sat Feb 14 2009 - 07:32:21 CST

On Fri, Feb 13, 2009, Antonios Samiotakis wrote:
>
> I am trying to apply improper torsions to one of my models.
> My problem is that no matter how many improper dihedrals
> I define, the Output for Dihedral potential does not change.

Amber does not internally distinguish between proper and improper
dihedrals, since they both have the same functional form.

You don't say how you are adding impropers. Note that improper terms in
a prep file are ignored by LEaP, which assigns improper terms based on
topology. This could explain your results, if that is indeed what you
are doing.

...dac

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