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''' | == Members == | ||
''' PhD Students''' | |||
* Hosein Geraili [https://www.mpikg.mpg.de/person/93901/6430004], currently based at my former workplace, the Max Planck Institute of Colloids and Interfaces in Golm, Germany. | |||
'''Former Members''' | |||
I have been fortunate to work with some wonderful students and post-docs. Here they are: | I have been fortunate to work with some wonderful students and post-docs. Here they are: | ||
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== Force field input files and tutorials == | |||
'''Parameters for the AMBER/GAFF force field''' | |||
The Amber/GAFF suite of force fields is widely used by the molecular simulation community. We have recently developed Lennard-Jones parameters [https://doi.org/10.1039/C7CP02557B] that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF. We provide improved parameters for the interaction of anions (carboxylates, sulfates, sulfonates, phosphates) with TIP3P water and with important cations (sodium, ammonium and primary amines). We ''strongly'' recommend using these parameters to adequately describe, e.g., salt bridges between acidic amino acids and lysine, and protein solvation at high NaCl concentrations. Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. | |||
To use these parameters, the simplest way is to email Ana Vila Verde for AMBER input files. | |||
If you want to learn how to modify Lennard-Jones parameters in the Amber force field, read through this tutorial. It explains how to: | |||
* Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. | |||
* Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins. | |||
Revision as of 10:28, 23 February 2021
The Soft Matter and Interfaces Group
On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time. You'll know I've pulled myself together when there is enough information here to make it useful (and when I'm confident enough to delete all the help links that tell me how to build a wiki...)
Dr. Ana Vila Verde (she)
WOS ResearcherID: H-7805-2013 ORCID: 0000-0003-0337-3972
Postal address University of Duisburg-Essen, Faculty of Physics (AG Wolf), Lotharstr. 1, 47057 Duisburg, Germany
Where I do my thinking: building MG, office 383
Email: ana.araujo-vila-verde@uni-due.de
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom, coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.
Topics
- Halophilic proteins
- Fluorinated proteins
Members
PhD Students
- Hosein Geraili [1], currently based at my former workplace, the Max Planck Institute of Colloids and Interfaces in Golm, Germany.
Former Members
I have been fortunate to work with some wonderful students and post-docs. Here they are:
- Dr. Ana Elisa Bergues-Pupo [2], currently at the Max Delbrück Center for Molecular Medicine in the Helmholtz Association
- Dr. João Robalo [3], currently at the Max Planck Institute for Colloids and Interfaces, Golm.
- Dr. Sadra Kashefolgheta [4]
- Dr. Chuanfu Luo, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
Force field input files and tutorials
Parameters for the AMBER/GAFF force field
The Amber/GAFF suite of force fields is widely used by the molecular simulation community. We have recently developed Lennard-Jones parameters [5] that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF. We provide improved parameters for the interaction of anions (carboxylates, sulfates, sulfonates, phosphates) with TIP3P water and with important cations (sodium, ammonium and primary amines). We strongly recommend using these parameters to adequately describe, e.g., salt bridges between acidic amino acids and lysine, and protein solvation at high NaCl concentrations. Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics.
To use these parameters, the simplest way is to email Ana Vila Verde for AMBER input files.
If you want to learn how to modify Lennard-Jones parameters in the Amber force field, read through this tutorial. It explains how to:
- Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins.
- Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.
Consult the User's Guide for information on using the wiki software.