Hi,
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,
-Dan
On Thu, Nov 29, 2018 at 4:43 AM Pietro Aronica
<pietroa.bii.a-star.edu.sg> 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
