What are the steps for linear interaction energy to calculate gibbs free energy in protein ligand system in gromacs?

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S. Xavier

What are the steps to install mmpbsa?

Should we necessarily install ABPS?

I did follow this link

http://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html

Got errors

Martin Klvana

Q molecular dynamics package: classical molecular dynamics, linear interaction energy (LIE), linear response approximation (LRA), free energy perturbation (FEP), and empirical valence bond (EVB) simulations.

http://xray.bmc.uu.se/~aqwww/q/

Thank you.

How do we arrive the co-efficient for linear interaction energy for Amber force field?

Eko Aditya Rifai

The initial values for alpha and beta in LIE equation are 0.18 and 0.5, respectively. Several groups use iterative LIE approach, i.e. training LIE model to obtain optimal alpha and beta values by using experimental data (e.g. refer to Article Improved Ligand-Protein Binding Affinity Predictions Using M...