Project ID: plumID:19.048
Name: Understanding Ligand Binding Selectivity in a Prototypical GPCR Family
Archive: https://github.com/Gervasiolab/Gervasio-Protein-Dynamics/raw/master/ADORA/ADORA_PLUMED_NEST.zip
Category: bio
Keywords: metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding
PLUMED version: 2.3.1
Contributor: Francesco Gervasio
Submitted on: 04 Jun 2019
Last revised: 11 Jun 2019
Publication: G. Mattedi, F. Deflorian, J. S. Mason, C. de Graaf, F. L. Gervasio, Understanding Ligand Binding Selectivity in a Prototypical GPCR Family, Journal of Chemical Information and Modeling 59, 2830–2836 (2019)

PLUMED input files

File Compatible with
A1_LUF.dat tested on v2.6 tested on master
A1_ZMA.dat tested on v2.6 tested on master
A2a_LUF.dat tested on v2.6 tested on master
A1_LUF.dat tested on v2.6 tested on master

Last tested: 13 Dec 2019, 20:32:23

Project description and instructions
These are the inpout files used to fully converge the free energy landscapes of two ligands (ZM241385, an A2aR-selective inverse agonist, and its dehydroxy derivative LUF545215) binding to two adenosine receptors (A1R and A2aR). The input files were used with GROMACS 5.1.4 and PLUMED 2.3.1 using the AMBER14SB force field, phospholipid topologies from LipidBook and ligands parameterized with Gaussian09 and Antechamber.

Submission history
[v1] 04 Jun 2019: original submission
[v2] 11 Jun 2019: fix labels input files

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plumeDnest:19.048