bioRxiv preprint doi: https://doi.org/10.1101/061184; this version posted July 11, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. FF12MC: A revised AMBER forcefield and new protein simulation protocol Yuan-Ping Pang Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, MN 55905, USA Corresponding author: Stabile 12-26, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA; E-mail address:
[email protected] Short title: FF12MC: A new protein simulation protocol Keywords: Protein folding; Protein dynamics; Protein simulation; Protein structure refinement; Molecular dynamics simulation; Force field; Chignolin; CLN025; Trp-cage; BPTI. bioRxiv preprint doi: https://doi.org/10.1101/061184; this version posted July 11, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. ABSTRACT Specialized to simulate proteins in molecular dynamics (MD) simulations with explicit solvation, FF12MC is a combination of a new protein simulation protocol employing uniformly reduced atomic masses by tenfold and a revised AMBER forcefield FF99 with (i) shortened C– H bonds, (ii) removal of torsions involving a nonperipheral sp3 atom, and (iii) reduced 1–4 interaction scaling