Project ID: plumID:22.029
Name: Angiotensin-1-7_Metadynamics
Archive: https://github.com/AmericaChi/Angiotensin-1-7_Metadynamics/archive/refs/heads/main.zip
Category: bio
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 (2022)

PLUMED input files

File Compatible with
metad.dat tested on v2.8 tested on master

Last tested: 22 Jun 2022, 17:09:59

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.

Submission history
[v1] 21 Jun 2022: original submission

Badge
Click on the image below and get the code to add the badge to your website!
plumeDnest:22.029