Project ID: plumID:23.010
Name: An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands
Archive: https://github.com/jacquecr23/GPCR-small-ligand-binding-protocol/raw/main/GPCR%20binding%20protocol.zip
Category: bio
Keywords: GPCR, binding free energy, free energy surface
PLUMED version: 2.5.3
Contributor: Timothy Clark
Submitted on: 06 Mar 2023
Publication: N. Saleh, P. Ibrahim, G. Saladino, F. L. Gervasio, T. Clark, An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G-Protein-Coupled Receptor Ligands. Journal of Chemical Information and Modeling. 57, 1210–1217 (2017)

PLUMED input files

File Compatible with
plumed.dat tested on v2.9 tested on master

Last tested: 28 Feb 2024, 06:48:53

Project description and instructions
Topologies for the receptors were generated using the AMBER99SB-ILDN force field. Ligands were parameterized using the generalized AMBER force field (GAFF) together with AM1-BCC partial charges.

Submission history
[v1] 06 Mar 2023: original submission

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plumeDnest:23.010