# Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 20 Oct 2014 02:08:30 -0400

On Mon, Oct 20, 2014 at 12:45 AM, Arun Srikanth <askforarun.gmail.com>
wrote:

> For Impropers I am not sure how amber defines the phi.
>

I answered that in my last email. It is defined exactly the same way as it
is for proper torsions (in fact, they are done in the same subroutine).

If I J L are on the same plane. It is the angle between I-J-L and I-K-J ?
>

​No, like proper torsions, it is the angle between the planes defined by
I-J-K and J-K-L​.

In lammps it is clearly defined this way.
>
> I,J,K,L - then the improper dihedral angle is between the plane of I,J,K
> and the plane of J,K,L. Note that because this is effectively a dihedral
> angle,
> Normally, the bonds I-J, I-K, I-L would exist for an improper to be defined
> between the 4 atoms.
>

​I'm not sure what your point is here? Actually in Amber, the 3rd atom is
the central atom (so the bonds I-K, J-K, and L-K exist).

I have to equivalently convert to this form. This I can do but I need to
> know how phi is defined for an improper in AMBER.
>

​I'm confused. You say above that LAMMPS has some weird I-J-L, I-K-J
definition for improper torsions, but then you say below that that the
improper angle is defined between I-J-K and J-K-L, and that you have to
convert to that latter definition.

Since Amber uses the same functional form for improper torsions as it uses
for proper torsions (unlike, for example, the CHARMM force field), the best
approa​ch IMO is to simply use the same subroutine for both kinds.

HTH,
Jason

```--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Oct 19 2014 - 23:30:02 PDT
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