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

From: Homeo Morphism <homeo.morphizm.gmail.com>
Date: Thu, 12 Mar 2020 14:16:23 +0300

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?

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Received on Thu Mar 12 2020 - 04:30:02 PDT
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