Hi everyone,
Just so people know, I have added to the user contributions section of
the website to include the AMBER ParmBSC0 nucleic acid parameters in
GROMACS 4.5.x format (see http://mmb.pcb.ub.es/PARMBSC0/ for further
details regarding these nucleic acid parameters). The modified dihedral
parameter conversion was validated through a comparison of single point
energies in GROMACS and AMBER (see the paper below for further details).
If you use these files we also ask that, in addition to the original
force field publications, you also cite:
Single-Stranded DNA within Nanopores: Conformational Dynamics and
Implications for Sequencing; a Molecular Dynamics Simulation Study
Andrew T. Guy, Thomas J. Piggot, and Syma Khalid
Biophysical Journal Volume 103, Issue 5, 5 September 2012, Pages 1028–1036
http://dx.doi.org/10.1016/j.bpj.2012.08.012
Cheers
Tom
--
Dr Thomas Piggot
University of Southampton, UK.
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