Albany 2019: 20th Conversation - Abstracts

category image Albany 2019
Conversation 20
June 11-15 2019
Adenine Press (2019)

Evaluation of the Current State of AMBER DNA Force Fields

Force field based modelling of nucleic acids has witnessed increasing interest in the past few years. Currently, several force field modifications for DNA simulations based on ff99 parameters are available in the AMBER suite of programs. Knowing how various conformations are described by available empirical force fields is crucial for molecular modelling of biomolecules, including DNA.

Several refinements of torsion potential (glycosidic potentials -ΧOL3, ΧOL4; backbone potentials - εϛOL1 and βOL1) have been suggested in our laboratory. All these refinements were derived using methodology that includes conformation-dependent solvation effects and are available in OL15 parameter package. These modifications significantly improved description of not only the canonical B-DNA structure but also the non-canonical systems, such as Z-DNA and guanine quadruplexes. Here, we report benchmark simulations of various representative DNA as well as a comparison of several (bsc0, bsc1, OL15) force fields. Furthermore, a comparative study of all 136 unique tetranucleotide steps using MD simulations with our latest OL15 force field, will be presented. We will provide a comprehensive analysis of the effect of BII substates on all B-DNA helical parameters and show how to reliably compare values from experiment and simulation.

The authors gratefully acknowledge the support by the Ministry of Education, Youth and Sports of the Czech Republic and Czech Science Foundation no. 17-16107S and by the Operational Programme Research, Development and Education – European Regional Development Fund project no. CZ.02.1.01/0.0/0.0/16_019/0000754.


    M. Zgarbova, J. Sponer, M. Otyepka, T. E. Cheatham III, R. Galindo-Murillo & P. Jurecka (2015). Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA. J. Comput. Theory Chem, 11, 5723-5736.

    M. Zgarbova, P. Jurecka, F. Lankas, T. E. Cheatham III, J. Sponer & M. Otyepka (2017). Influence of BII Backbone substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences. J. Chem. Inf. Model., 57, 275-287.

Marie Zgarbová 1
Michal Otyepka 1
Jiří Šponer 1,2
Petr Jurečka1

1 Regional Centre of Advanced Technologies and Materials
Department of Physical Chemistry
Faculty of Science
Palacký University
tř. 17 listopadu 12
771 46 Olomouc, Czech Republic

2 Institute of Biophysics of the Czech Academy of Sciences
Královopolská 135
612 65 Brno, Czech Republic

Ph: (+420) 585 634 766
Fx: (+420) 585 634 761
Email: marie.zgarbova@upol.cz