Re: [AMBER] dihedral in parmtop: negative third index vs ICP(H)

From: Hannes Loeffler <>
Date: Fri, 5 Sep 2014 10:42:44 +0100

On Thu, 4 Sep 2014 07:11:01 -0400
Jason Swails <> wrote:

> On Thu, Sep 4, 2014 at 4:57 AM, Hannes Loeffler
> <> wrote:
> > Hi,
> >
> > I have the following entry in a parmtop file of mine
> >
> > %FORMAT(10I8)
> > 3 6 -9 12 1
> >
> > the third index indicates that the non-bonded interactions between
> > the 1-4 atoms should not be computed (this particular torsion
> > appears only once in the file = single term dihedral). The
> > dihedral is from four C atoms in the phenyl ring of toluene
> > adjacent to the methyl side group.
> >
> > Now I understand that to allow mixed scaling the new flags %FLAG
> > SCEE_SCALE_FACTOR and %FLAG SCNB_SCALE_FACTOR have been introduced
> > some time in the past to allow explict recording of scaling factors.
> > This means, I think, that the fifth number above (ICP) points into
> > the first entry of these flags (the web documentation of the parmtop
> > format mentions arrays "ONE_SCEE" and "ONE_SCNB"). The values there
> > are not zero possibly implying that 1-4 scaling should be carried
> > out contrary to the negative third index.
> >
> > So, obvious question: what is really going to happen? My first
> > guess would have been that ICP(H) overwrites the negative index and
> > scaling is indeed carried out in sander/pmemd.
> >
> ​No, scaling is not carried out -- those 1-4 interactions are excluded
> entirely. The negative index determines whether or not to carry out
> the 1-4 electrostatic energy (of course you can change that negative
> to a positive and check that the energy does, indeed, change by the
> exact amount of the scaled 1-4 electrostatic and van der Waals
> interactions for that 1 pair).

So the simple rule is: negative third index takes precedence over

> ​Rings are, IMO, the trickiest part of a topology to handle
> "correctly" in the force field. For all multi-term dihedrals, there
> is _never_ a case where the first N-1 terms of an N-term dihedral
> should trigger computing the 1-4 interactions, so those third indexes
> are always negative and a SCEE/SCNB value of 0 can be safely applied
> to those terms. In a ring, as you pointed out, it is possible (and
> quite common) to have torsions specified by a single term, but whose
> interactions are not computed either because they are included in a
> different 1-4 interaction (in the case of 6-member rings) or they are
> excluded because they are 1-3 partners (in the case of 5-member
> rings). However, those atom types are not guaranteed to exist in
> just 6-member or 5-member rings, so you can't guarantee that their
> interactions will never need to be computed. As a result, you can't
> broadly assume their SCEE/SCNB values to be 0.​

The only complication then seems to me to be the 5-rings because the
decision has been made to exclude possible 1-4 pairs as they are also
in 1-3 relationship (from a recent conversation with a colleague I had
the impression that CHARMM does not do that). Otherwise, the simple
procedure would be to enumerate all 1-4 pairs and eliminate all
duplicates afterwards.

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Received on Fri Sep 05 2014 - 03:00:03 PDT
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