README.md

Parameters for DHI eumelanin

• Parameters for DHI eumelanin from the paper

  Free Energy and Stacking of Eumelanin Nanoaggregates. Soltani, Sepideh; Sowlati-Hashjin, Shahin; Tetsassi Feugmo, Conrard Giresse; Karttunen, Mikko. J. Phys. Chem. B 126, 1805–1818, (2022).
  Web: https://doi.org/10.1021/acs.jpcb.1c07884

  Please see the paper for the details of the minimization process.

  • List of parameters (plain text). The coordinates (x, y and z) are given in nanometers.
  • Corresponding .itp file (for Gromacs)
  • Corresponding .gro file (for Gromacs)
  • Figure showing the atom numbering

Parameters for DHICA eumelanin

The article:

Structural Investigation of DHICA Eumelanin Using Density Functional Theory and Classical Molecular Dynamics Simulations. Soltani, Sepideh; Sowlati-Hashjin, Shahin; Tetsassi Feugmo, Conrard Giresse; Karttunen, Mikko. Molecules 27, 8417 (2022).
Web: https://doi.org/10.3390/molecules27238417.

• itp file for charged DHICA (for Gromacs)
  • Corresponding .gro file (for Gromacs)
• itp file for charged DHICA (for Gromacs)
  • Corresponding .gro file (for Gromacs)

Parameters for drug molecules studied with DHI and DHICA

• Parameters from the manuscript

  A Computational Investigation of Eumelanin-Drug Binding in Aqueous Solutions, Sepideh Soltani, Anupom Roy, Arto Urtti, and Mikko Karttunen

Abbrevations:

• OTX - Chloroquine
• LFX - Levofloxacin
• TIM- Timolol
• MTX - Methotrexate
• DIC - Diclofenac