Re: [AMBER] Restraint-like bonds using ParmEd setBond?

From: Jason Swails <>
Date: Tue, 2 Nov 2021 16:52:09 -0400

In general terms this is impossible, and that's because the PME code
computes the exceptions from the lists of bonds, angles, and torsions. If
you used the GB code (either using a GB model or setting igb=6 to get
vacuum electrostatics without periodic boundary conditions), then you can
hack the exclusion list in the topology file to achieve what you want.

I think you can do what you want if you're willing to use OpenMM (because
you can control the exceptions very fine-grained), but not within sander or


On Mon, Nov 1, 2021 at 2:32 PM Brian Radak <> wrote:

> My understanding is that adding new bonds with ParmEd is akin to adding new
> force field terms such that nonbonded exclusions are updated in the
> topology. The only difference is that a bond does not necessitate angles
> and dihedrals as in tleap (or a defined bond type). This seems to be
> verified by "just doing it" and checking that the energy difference is not
> in the BOND term only.
> My question is - is there a way _not _ to update the exclusions so that the
> new term is exactly like a harmonic restraint? This would trick the
> bookkeeping in alchemical calculations, which apply a lambda factor to
> nmropt terms.
> Cheers,
> Brian
> _______________________________________________
> AMBER mailing list

Jason M. Swails
AMBER mailing list
Received on Tue Nov 02 2021 - 14:00:02 PDT
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