[AMBER] free energy calculation for restraining ligand

From: Sukanya Sasmal <sasmals.uci.edu>
Date: Thu, 29 Nov 2018 18:27:53 -0800


I am trying to calculate free energy required to restrain a ligand.

So far, I have tried using TI implemented in Amber18, where I described the
unrestrained and restrained ligand in the same prmtop file and used a
lambda parameter to go from the unrestrained to the restrained state.
However, the dV/dlambda values which I got are close to zero.

I am currently considering running two separate MD simulations with and
without restraints and then using MBAR to estimate energies.

Is there any other way this can be done, particularly using TI ?

Thanks for your help,

Sukanya Sasmal
Postdoctoral Scholar
David Mobley Lab
UC Irvine
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Received on Thu Nov 29 2018 - 18:30:02 PST
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