Post-simulation MM/GBSA analysis was performed by using the thermal_MMGBSA.py script of the Prime/Desmond module of the Schrodinger suite 2020-3 [27 (link),28 (link)]. From each MD trajectory, every 10th frame was extracted from the last 50 ns of simulated trajectories, averaging over 50 frames, for binding free energy calculations of teicoplanin. The Prime MM/GBSA method uses rule of additivity wherein total binding free energy (Kcal/mol) represents a summation of individual energy modules like coulombic, covalent, hydrogen bond, van der Waals, self-contact, lipophilic, solvation, and π-π stackings of ligand and protein.[38] (link)
Prime desmond module
Manufactured by Schrödinger
The Prime/Desmond module is a software package developed by Schrödinger for molecular modeling and simulation. It provides a framework for performing a variety of computational chemistry tasks, including structure-based drug design, molecular dynamics simulations, and quantum mechanical calculations. The module offers a range of tools and algorithms for tasks such as ligand docking, molecular property prediction, and protein structure analysis.
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Lab products found in correlation
2 protocols using prime desmond module
1
MM/GBSA Analysis of Teicoplanin Binding
2
MM-GBSA Analysis of Binding Energies
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Post-simulation MM-GBSA analysis was carried out. The thermal_MMGBSA.py script of the Prime/Desmond module of the Schrödinger suite was used. The post-simulation MM-GBSA analysis of free binding energy calculation was carried out with the generation of 0–1000 frames. Two hundred frames were processed and analyzed throughout the MM-GBSA calculation of 100 ns MDS data. The binding free energies (kcal/mol) were then calculated.
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