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2.1.4. Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) Analysis

AM Alessia Marconi
GG Giulia Giugliano
MG Matteo Di Giosia
TM Tainah Dorina Marforio
MT Michele Trivini
ET Eleonora Turrini
CF Carmela Fimognari
FZ Francesco Zerbetto
EM Edoardo Jun Mattioli
MC Matteo Calvaresi
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Using CPPTRAJ [59], one frame every 0.1 ns was retrieved from the MD trajectories and used as input for the MM-GBSA analysis. MM-GBSA analysis was carried out with the MMPBSA.py [60] module, determining the binding affinity between mTHPC and the different proteins. Electrostatic and van der Waals (vdW) interactions were calculated considering an infinite cut-off. The polar solvation term was calculated using the Generalized Born (GB) model, whereas the non-polar solvation term was determined using solvent-accessible, surface-area-dependent terms.

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