Data of the publication: Buffer-specific Interactions of Imidazolium with Elastin-like Polypeptides

Keil, Julia; van der Vegt, Nico

Open Access

Data of the publication: Buffer-specific Interactions of Imidazolium with Elastin-like Polypeptides

Files

Data-Paper-Buffer_specific_Interactions_of_Imidazolium_with_Elastin_like_Polypeptides.zip (15.35 GB)

Date

2025-06-17

Type

Software
Image
Dataset
Workflow

Authors

Keil, Julia

van der Vegt, Nico

Description

This folder summarizes the important files used for the simulations and analyses related to the publication 'Buffer-specific Interactions of Imidazolium with Elastin-like Polypeptides'. They are organized as follows: Folder 'cluster' contains all important files from the cluster. This includes all simulation files (except from trajectories '.xtc' and '.edr') and all analysis files. Folder 'local' contains all important files from the local computer. This includes all additional analysis files and the files needed for the plotting of the graphs. Subfolder '0.Parametrization_Buffer' contains all data related to the reparametrization of the buffer particles. Subfolder '1.Parametrization_Aminoacids' contains all data related to the reparametrization of the amino acids. Subfolder '1.Parametrization_Buffermolecules' contains all data related to the parametrization of IMI. 'BUF' contains data for the parametrization of buffer particles 'ARG' contains data for the parametrization of arginine 'ASP' contains data for the parametrization of aspartic acid 'GLU' contains data for the parametrization of glutamic acid 'LYS' contains data for the parametrization of lysine 'IMI' contains data for the parametrization of imidazolium '0.Preparation', '1.Equilibration', and '2.Parametrization-1' contain data for the thermodynamic integration step '3.Parametrization-2', '4.Parametrization-3', ... contain the data for the following sampling simulations, including the reweighting '5.Titration' or '6.Titration' contain the data for the following test titration simulations Subfolder '2.Preparation_ELPs' contains the data for the preparation of infinitely long ELPs '0.Structure_Preparation' and '1.Infinite_Strand' contain the preparation of the structure and topology file for the infinitely long chains '2.Simulation' contains longer simulations to equilibrate and test the structure of the infinitely long chains Subfolder '3.Simulations_ELPs_IMI' contains the data for the simulations of solutions with ELPs and IMI 'IMI_6' contains the data for systems containing 6 IMI 'IMI_30' contains the data for systems containing 30 IMI 'IMI_60' contains the data for systems containing 60 IMI '0.Preparation' contains data of the preparation of the systems '1.Equilibration' contains data of the equilibration of the systems '2.cpH-Simulation' contains data of the final sampling simulation at constant pH 'IMI-water' contains the data for a binary system of IMI and water (same system as the others, but without the ELP) (needed for the calculation of Kirkwood-Buff-Integrals between water and IMI and between different IMIs) 'ELP-GLY-urea', 'ELP-SER-urea', 'urea-water' contain the same simulations as 'ELP-GLY', 'ELP-SER', 'IMI-water', but with urea instead of IMI Subfolder '4.Analysis_ELPs_IMI' contains the data of the analysis of the long sampling simulations 'IMI_6' contains the data for systems containing 6 IMI 'IMI_30' contains the data for systems containing 30 IMI 'IMI_60' contains the data for systems containing 60 IMI '1.Preferential_Binding-whole_peptide' contains data for the analysis of preferential binding coefficients around the whole peptide (reported 'per 5-mer') '2.Preferential_Binding-individual_aminoacids' contains data for the analysis of preferential binding coefficients around the individual amino acids within the 5-mer (reported in 'per amino acid') '3.Hydrogen_Bonding_Sidechains' contains data for the analysis of hydrogen bonds to the polar and charged side chains of amino acid X '4.Hydrogen_Bonding_Backbone' contains data for the analysis of hydrogen bonds to the backbone of the ELP '5.RDF-whole_peptide' contains data for the analysis of the RDF around the whole peptide '6.RDF-individual_aminoacids' contains data for the analysis of the RDF around the individual amino acids within the 5-mer (data were not reported, as the long range behavior of these curves is very poor and corrections are complicated if titratable groups are involved) '7.Numbers-Distance' contains data for the analysis of cumulative numbers of water, protonated, and deprotonated IMI around the ELP (they are needed for the conversion of the numbers of hydrogen bonds into probabilities) '8.RDF-Xxx-IMI' contains data for the analysis of RDFs between the COMs of planar groups in Arg/Phe and IMI (needed for the stacking analysis) '8.Stacking' contains data for the analysis of stacking interactions between Arg and IMI or Phe and IMI '1.KBI-SOL-BUF' contains data for the analysis of Kirkwood-Buff-Integrals between water and IMI/urea '2.KBI-BUF-BUF' contains data for the analysis of Kirkwood-Buff-Integrals between two IMI or two urea molecules 'Figures-Paper' contains figures included in the paper Subfolder 'Figures-Paper-Parametrization' contains figures included in the SI for the discussion of the parametrization