Project ID: plumID:22.029
Keywords: Metadynamics, Angiotensin-(1-7), peptide
PLUMED version: 2.5
Contributor: L.-América Chi
Submitted on: 21 Jun 2022
Publication: L. A. Chi, S. Asgharpour, J. Correa-Basurto, C. R. Bandala, M. Martínez-Archundia, Unveiling the G4-PAMAM capacity to bind and protect Ang-(1-7) bioactive peptide by molecular dynamics simulations. Journal of Computer-Aided Molecular Design. 36, 653–675 (2022)
PLUMED input files
Last tested: 28 Mar 2023, 07:04:54
Project description and instructions
These scripts can be used to run Metadynamics simulation of Angiotensin-(1-7) vasoactive peptide in order to explore its conformational landscape in solution at neutral pH. Collective variables are a kind of HBs and gyration radius. If useful for your project, please cite this preprint. Call via
bash run.sh. This script needs md.tpr, index_metad2.ndx and metad.dat files in the root directory. md.tpr should be created in its corresponding GROMACS version by using .itr, .top, .mdp and .pdb files. Force field used can be found here as a .zip file. FF reference Horta, B. A., et al (2016). A GROMOS-compatible force field for small organic molecules in the condensed phase The 2016H66 parameter set. J. Chem. Theory Comput. 2016, 12, 8, 3825–3850. Scripts require a proper GROMACS patched with PLUMED installed. This simulations were run on a GROMACS 2016.5 and PLUMED Version 2.5.0.
[v1] 21 Jun 2022: original submission
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