Re: [AMBER] What's the least biased way to stop a molecule from crossing a periodic boundary?

From: Carlos Simmerling <>
Date: Thu, 12 Mar 2020 07:48:44 -0400

Maybe the problem isn't wrapping, but the actual periodic box. Are you
saying that the 2 sides of your receptor are so close in the periodic
lattice that it can easily move between the intra and extracellular sides?
Perhaps the box is too small. You could increase your box size (probably
needed if they are this close since it isn't a good model). To me the
flatwell resrraint you have tried seems reasonable. It only introduces bias
in the region away from your interest. Of course it does impact things like
binding equilibrium, but you are not likely to get converged values for
that in any case. Just make sure that your restraint is zero regardless of
the area near your binding site. 40A sounds ok to me.

On Thu, Mar 12, 2020, 7:21 AM Carlos Simmerling <>

> Why not just disable wrapping in the mdin file? Iwrap =0
> On Thu, Mar 12, 2020, 7:16 AM Homeo Morphism <>
> wrote:
>> I'm modelling interactions of a ligand with a GPCR-receptor under ligand's
>> free diffusion. Receptor is membrane-bound. And the ligand is initially
>> placed in the solvent on the extracellular side of the receptor.
>> Naturally, in some simulations the ligand crosses the periodic boundary
>> that separates extracellular part of the receptor from the intracellular
>> one and starts interacting with receptor's intracellular loops.
>> I've been dealing with this by introducing an nmr distance restraint that
>> kicks in once the ligand is, say, 40 angstroms from the receptor's
>> extracellular loops and slightly pushes it toward certain extracellular
>> loop's amino acid. I make the force which the ligand is pushed with small
>> by setting rk3-parameter equal to 0.5 or 0.1.
>> I still believe, however, that this introduces a bias - the ligand is
>> pushed, however gently, toward the extracellular loops and a certain amino
>> acid in particular. Since the ligand's interactions with extracellular
>> loops is exactly what I'm trying to model, I'd like to avoid this push.
>> But without this kind of restraints how else would I stop the ligand from
>> crossing the periodic boundary and interacting with the intracellular
>> parts
>> of the receptor?
>> Thanks.
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Received on Thu Mar 12 2020 - 05:00:02 PDT
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