Re: [AMBER] pi-pi And Aromatic Interactions

From: Chris Neale <>
Date: Thu, 18 Oct 2018 21:27:05 -0600

Be careful... atomistic force fields typically don't have any pi electron
effects in the Hamiltonian, so why would you analyze for them? In fact,
most atomistic force fields do a pretty terrible job at pi-based effects
like aromatic stacking. Same goes for cation-pi interactions.

On Thu, Oct 18, 2018 at 8:08 PM Meng Wu <> wrote:

> Dear all,
> I have MD for my channel protein and substrate molecules and I have
> used the "lie" command to calculate the EELEC and EVDW terms. Now I want to
> analysis like the pi-pi interactions or aromatic interactions between the
> substrates and protein & residue to residue in protein, could anybody give
> me some suggestions? Thank you in advance!
> Best regards,
> Meng Wu
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Received on Thu Oct 18 2018 - 20:30:03 PDT
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