AMBER Archive (2009)

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

From: Carlos Simmerling (
Date: Wed Sep 09 2009 - 05:23:31 CDT

not sure in this case, but sometimes I set PK to zero for a term to
make sure that it doesn't have any energy for that periodicity- for
example, to override a generic that might have been applied.

On Wed, Sep 9, 2009 at 4:00 AM, Loeffler, Hannes
(STFC,DL,CSE)<> wrote:
> Hi,
> 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?
> Cheers,
> Hannes.
> --
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