Re: [AMBER] pmemd simulation

From: David Cerutti <>
Date: Wed, 13 May 2020 02:52:06 -0400

pmemd will describe that anion :: pi interaction the same way it describes
any other non-bonded interaction: Lennard-Jones 6-12 plus electrostatic
interactions between the monopoles. I knew about cation :: pi
interactions, but I confess I hadn't heard of special behavior in anion ::
pi interactions. The disassociation of this interaction is not
surprising--it is a very tough task to balance the affinity of an anion for
any hydrophobic group with its affinity for water. In all likelihood, the
charge model is just not up to the task of modeling the induced
polarization that you might be getting in real life, to say nothing of
other effects involving the actual pi system where we don't currently model
any monopoles.


On Wed, May 13, 2020 at 2:01 AM Sofia Vasilakaki <>

> Dear all,
> I would like to ask how the pmemd describe the interaction between an
> aromatic ring and an anion.
> What I have in my X-ray structure is an aromatic ring in close proximity
> to an -Cys-S-S (-1) anion. The anion is closer to one of the carbon atoms
> which, based on QM calculations, has a positive partial charge. During
> the simulation, the aromatic ring moves away from the anion and, in some
> cases, the molecule goes off to the solvent, although in the initial
> (X-ray) pose is very well packed in the active site.
> Any suggestions why this happening and how I could keep the molecule in
> place.
> Thank you,
> Sofia
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Received on Wed May 13 2020 - 00:00:03 PDT
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