Raffaele Fiorentini
Kurt Kremer
Raffaello Potestio
2020-02-12
<p><strong>README file for the project files provided as supporting information to the manuscript "Ligand-protein interactions in lysozyme investigated through a dual-resolution model"</strong></p>
<p>February 12, 2020</p>
<p>Authors: Raffaele Fiorentini, Kurt Kremer and Raffaello Potestio</p>
<p>================================</p>
<p>Overview</p>
<p>The dataset is organised in three (compressed) subfolders (see the tree diagrams in each section):</p>
<p>- annihilation<br>
- decoupling<br>
- density</p>
<p>The figure deltaG_binding_ann_dec_comparison.png shows the results of binding free energy calculations comparing the values obtained both for annihilation and decoupling.</p>
<p>The figure deltaG_binding_annih_gromacs_espp.png displays the results for Binding FE, comparing the values obtained in GROMACS and ESPResSo++.</p>
<p>The README.pdf file contains detailed information about these folders and their content.</p>
<p>================================</p>
<p>The "annihilation" folder contains all results concerning the calculation of binding free energy in case of annihilation and it is divided in two parts: </p>
<p>- complex<br>
- ligand</p>
<p>In "complex" are reported the results of Ligand-Protein FE both in ESPResSo++ and GROMACS. All simulations are fully-atomistic. </p>
<p>In "ligand" are reported the results of ligand solvation free energy both in ESPResSo++ and GROMACS. All simulations are fully-atomistic. </p>
<p>====</p>
<p>The "decoupling" folder contains all results concerning the calculation of binding free energy in case of decoupling and it is divided in three parts: </p>
<p>- complex-DualRes<br>
- complex-FullyAT<br>
- ligand</p>
<p>In "complex-DualRes" are reported the results of Ligand-Protein FE only in ESPResSo++ (GROMACS cannot do decoupling). The system is simulated in Dual-Resolution. It is possible to find the trajectory files in the sub-directories "lambdaindex-0" and "lambdaindex-30".</p>
<p>In "complex-fullyAT" are reported the results of Ligand-Protein FE only in ESPResSo++. The system simulated is fully-atomistic. It is possible to find the trajectory file in the sub-directories "lambdaindex-0" and "lambdaindex-30".</p>
<p>In "ligand" are reported the results of ligand solvation free energy only in ESPResSo++. All simulations are fully-atomistic. It is possible to find the trajectory file in the sub-directories "lambdaindex-0" and "lambdaindex-20".</p>
<p>====</p>
<p>The "density" folder contains the data for the tuning of the c parameter of the steric repulsion among residues. This parameter is tuned so that the water density attains the value computed in all-atom simulations.</p>
https://doi.org/10.5281/zenodo.3665677
oai:zenodo.org:3665677
Zenodo
https://zenodo.org/communities/eu
https://doi.org/10.5281/zenodo.3665676
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Project files provided as supporting information to the manuscript "Ligand-protein interactions in lysozyme investigated through a dual-resolution model"
info:eu-repo/semantics/other