Re: [AMBER] Linear Interaction Energy

From: Daniel Roe <>
Date: Mon, 3 Dec 2018 15:50:03 -0500


I'm not very familiar with FEW so I'll leave that to others to answer,
but there is a very simple LIE calculation action in CPPTRAJ (vi the
'lie' command) that was designed primarily to look at ligand/receptor
interactions. Currently it only does very simple electrostatics and
LJ, although I'm hoping to improve that in the future. See the manual
for full details. Hope this helps,


On Thu, Nov 29, 2018 at 4:43 AM Pietro Aronica
<> wrote:
> Dear all,
> I was looking to set up some linear interaction energy (LIE) analysis of
> my system, having previously performed MMPBSA/GBSA. I read through the
> tutorial A24, but I had some questions before I start the work in earnest.
> 1. The tutorial says that LIE employs the 3-trajectory setup, where it
> uses independent simulations of ligand, receptor and complex. Does this
> approach have the same drawbacks as it does for MMPBSA/GBSA, where the
> 1-trajectory approach is more common? What if the 1-trajectory approach
> was used for LIE?
> 2. The tutorial explains how to run LIE through FEW. Is this necessary?
> Can I use LIE to analyse trajectories I already have or do I need to do
> it through FEW?
> If I have misunderstood something let me know.
> Thanks in advance,
> Pietro Aronica
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Received on Mon Dec 03 2018 - 13:00:02 PST
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