Re: [AMBER] Setting exclusions correctly

From: Jason Swails <>
Date: Wed, 15 Oct 2014 23:42:33 -0400

On Tue, Oct 14, 2014 at 6:38 PM, Arun Srikanth <> wrote:

> Thanks Dan and Jason.
> Let's say one guesses the dihedrals based on the bond topology (two bonds
> that share a bond). Will the dihedrals thus guessed be a subset of the
> dihedrals guessed by GAFF forcefield obtained by using (print
> dihedrals).
> In other words,
> if one finds the unique dihedrals form the dihedrals list will this number
> be equal to the dihedrals guessed on bond topology ?

​Yes. You can make this *untrue* by using the "deleteDihedral" command in
ParmEd to remove particular torsion terms. But with any prmtop that comes
out of tleap, the unique dihedrals in the DIHEDRALS_INC_HYDROGEN and
DIHEDRALS_WITHOUT_HYDROGEN will be the same as the dihedrals you determine
from the bond connectivity.

In this list of unique torsion terms, the only ones whose 1-4 nonbonded
terms will *not* be calculated will be those torsions in 4-, 5-, and
6-member rings, as I've described before.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Oct 15 2014 - 21:00:02 PDT
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