Project ID: plumID:21.018
Name: Localized Volume-based Metadynamics
Category: bio
Keywords: LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification
PLUMED version: 2.6
Contributor: Riccardo Capelli
Submitted on: 04 May 2021
Last revised: 09 Dec 2021
Publication: Q. Zhao, R. Capelli, P. Carloni, B. Lüscher, J. Li, G. Rossetti, Enhanced Sampling Approach to the Induced-Fit Docking Problem in Protein–Ligand Binding: The Case of Mono-ADP-Ribosylation Hydrolase Inhibitors. Journal of Chemical Theory and Computation. 17, 7899–7911 (2021)

PLUMED input files

File Compatible with
input/MacroD2_I189R_input/metad_35ang.dat tested on v2.8 tested on master
input/MacroD1_para_input/metad_35ang.dat tested on v2.8 tested on master
input/MacroD2_Y190N_input/metad_35ang.dat tested on v2.8 tested on master
input/MacroD2_para_input/metad_35ang.dat tested on v2.8 tested on master
input/MacroD2_sphere_input/metad_35ang.dat tested on v2.8 tested on master
plumed_metad/metad_35ang_sphere.dat tested on v2.8 tested on master
plumed_metad/metad_35ang_para.dat tested on v2.8 tested on master
plumed_reweight/reweight_rho_hb.dat tested on v2.8 tested on master

Last tested: 22 Jun 2022, 17:39:04

Project description and instructions
All the input files to simulate MacroD1, MacroD2, and the studied mutants of MacroD2 (Y190N and I189R) in complex with ADPr using Gromacs 2019.2 are in the input folder. In the plumed_metad folder 2 reference input files for parabolic and 1/3 sphere volume restraint are available. In the plumed_reweight folder the reweight input file is available.

Submission history
[v1] 04 May 2021: original submission
[v2] 04 Aug 2021: updated doi
[v3] 09 Dec 2021: updated doi

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