Project ID: plumID:23.035
Name: An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors
Archive: https://github.com/jacquecr23/Peptide-ligands-binding-protocol/raw/main/Peptide-ligands-binding-unbinding-protocol.zip
Category: bio
Keywords: G protein coupled receptor, peptide ligands, metadynamics, multiple-walker
PLUMED version: 2.7.3
Contributor: Timothy Clark
Submitted on: 30 Aug 2023
Publication: J. C. Calderón, E. Plut, M. Keller, C. Cabrele, O. Reiser, F. L. Gervasio, T. Clark, Extended Metadynamics Protocol for Binding/Unbinding Free Energies of Peptide Ligands to Class A G-Protein-Coupled Receptors. Journal of Chemical Information and Modeling. 64, 205–218 (2023)
PLUMED input files
| File | Compatible with |
|---|---|
| Y4R_SRS_Gi/MW-WT-MetaD_Y4R-SRS-Gi/plumed.dat |   |
Last tested: 22 Apr 2024, 20:41:52
Project description and instructions
Multiple-walker metadynamics simulations were performed using GROMACS 2021.4 with the PLUMED 2.7.3 plug-in. Topologies for the receptor, peptides, and G protein were generated using the AMBER99SB-ILDN force field.
Submission history
[v1] 30 Aug 2023: original submission
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