Project ID: plumID:23.005
Name: A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs
Archive: https://github.com/dorotheagobbo/5HT1_NEST/raw/main/apo-5HT1A.zip
Category: bio
Keywords: metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A
PLUMED version: 2.5.3
Contributor: Timothy Clark
Submitted on: 13 Feb 2023
Publication: J. C. Calderón, P. Ibrahim, D. Gobbo, F. L. Gervasio, T. Clark, General Metadynamics Protocol To Simulate Activation/Deactivation of Class A GPCRs: Proof of Principle for the Serotonin Receptor. Journal of Chemical Information and Modeling. 63, 3105–3117 (2023)

PLUMED input files

File Compatible with
apo-5HT1A/plumed.dat tested on v2.9 tested on master
apo-5HT1A/plumed_reweight_2D_microsw_5ht1a_rec.dat tested on v2.9 tested on master
apo-5HT1A/plumed_reweight_microsw_5ht1a_rec.dat tested on v2.9 tested on master

Last tested: 17 Apr 2024, 07:16:17

Project description and instructions
Multiple-walkers Metadynamics simulations were performed using GROMACS 2019.4 with the PLUMED 2.5.3 plug-in. 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] 13 Feb 2023: original submission

Badge
Click on the image below and get the code to add the badge to your website!
plumeDnest:23.005