AMBER Archive (2009)

Subject: Re: [AMBER] PK zero for specific dihedral and parmchk

From: case (case_at_biomaps.rutgers.edu)
Date: Wed Sep 09 2009 - 06:32:51 CDT

On Wed, Sep 09, 2009, Loeffler, Hannes (STFC,DL,CSE) wrote:
>
> I have used parmchk (AmberTools 1.2) to check for missing parameters
> (gaff) in a cyclo hexen derivative and got a few dihedrals within the
> ring reported as missing. What puzzles me is that PK has been set to
> zero for all of them. My understanding is that this would lead to zero
> energy (and zero forces) which doesn't make sense to me. Is there a
> reason why parmchk sets them to zero?

The zero is just a place holder, to show you where the "real" result should
go.

...dac

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