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

From: Jason Swails <>
Date: Thu, 4 Sep 2014 07:11:01 -0400

On Thu, Sep 4, 2014 at 4:57 AM, Hannes Loeffler <>

> 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

​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.​

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Sep 04 2014 - 04:30:04 PDT
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