Re: [AMBER] Regarding impropers from and guessing from bond topology

From: Arun Srikanth <>
Date: Mon, 20 Oct 2014 00:16:10 -0400

Thanks i will keep point [1] in mind.

Two questions

In amber,

 1. If I have a dihedral let's say I-J-K-L. How is phi calculated in the
dihedral potential expression. Is it the angle between the planes
I-J-K and J-K-L

2. How is phi defined for an improper I-J-K-L with K as the central atom


On Sun, Oct 19, 2014 at 12:52 AM, Jason Swails <>

> On Oct 18, 2014, at 11:20 PM, Arun Srikanth <> wrote:
> > Thanks Jason and Daniel. I am using topotools (A plugin in vmd). You can
> > load the mol2 file generated by antechamber in vmd.
> >
> > Then use topotools guessimproper in vmd to get the impropers for the
> > system. The improper definition it employs is
> >
> > "Guess improper angles. Are defined for atoms that are bonded to
> *exactly*
> > 3 atoms when they form a near flat structure. The tolerance flag can be
> > used as a cutoff for what is to be considered as "flat" and what not. “
> This is not the same criteria as that used for tleap, which my last email
> described. Now I’m not *absolutely* positive that what I said there is the
> actual algorithm implemented in tleap for determining potential candidates
> for improper torsions, but I believe it is close enough. In any case,
> there should not be any geometry-based decisions that are made by tleap,
> since then your parametrization will depend on the starting conformation of
> the molecule (not good).
> Also, not every *potential* improper site needs to be given an improper
> term to keep it planar (and, as Dave said before, “planarity” isn’t even a
> requirement -- it’s just the typical use for improper torsions).
> So the algorithms in VMD guessimproper and tleap are quite different.
> While I would expect them to find many of the same 4 atoms as “improper
> centers”, do not expect full agreement between them.
> Also, the name of the VMD tool is telling -- _guess_impropers; that’s all
> it is, a guess based on simple geometric measurements.
> > You can now compare the two impropers. They are not the same.
> >
> > I checked this for dihedrals. Some how the dihedrals from topotools and
> > unique dihedrals from leap are matching.
> This I would expect. Proper torsions are defined between 4 atoms that are
> connected by 3 sequential bonds. Every proper torsion is required to have
> a parameter by tleap, so there is no “guesswork” in this case.
> >
> > So My question is
> >
> > 1. WIll the connectivity of the dihedrals, impropers guessed from bond
> > topology and the connectivity of the dihedrals, impropers assigned by
> leap
> > (based on parametrization, leave out the multi terms or the duplicates)
> > match always ?
> You can’t guess impropers simply from bond connectivities. You can guess
> proper torsions based on bond connectivities. But any two conformations of
> the same molecule (regardless of how ridiculous those conformations may be)
> will be parametrized identically. [1]
> HTH,
> Jason
> [1] This does not include charge derivation, which depends sometimes
> strongly on the conformation; so choose a good one(s).
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sun Oct 19 2014 - 21:30:02 PDT
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