[AMBER] Linear Interaction Energy

From: Pietro Aronica <pietroa.bii.a-star.edu.sg>
Date: Thu, 29 Nov 2018 17:43:51 +0800

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 Thu Nov 29 2018 - 02:00:02 PST
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