The AMBER simulations were carried out with the ff9931 (link), bsc08 (link), χOL39 ,10 (link) and χOL4 (this work) versions of the Cornell et al. force field.5 Bsc0 introduced significant modification to α/γ backbone torsional parameters essential for stability of B-DNA simulations. The χOL3 parametrization modified the χ glycosidic torsions to stabilize RNA simulations. While χOL3 modification can be combined with either ff99 or bsc0 for RNA, it works best in combination with bsc0. All DNA simulations must include bsc0.
ParmχOL4 is a new version of the χ-profile which aims to improve description of the syn region and syn-anti balance while not deteriorating the B-DNA simulations by the anti to high-anti region. The syn region of χOL4 profile differs from that of the RNA χOL3 force field in that it provides narrower and somewhat deeper syn valley than χOL3, thus suppressing the excessive population of χ syn angles in the region of 90–110°. This is a result of using a deoxyribonucleoside model compound instead of the ribonucleoside one for fitting, i.e., the difference is consistent with the primary QM data. When compared to the ff99 force field, χOL4 shifts the syn minimum to the higher χ values by about 10° and apparent are also differences in the barrier heights (Figure 2). Also, the syn minimum is somewhat deeper, which is an opposite trend compared to the χOL3 modification. While the syn region was fitted to the deoxyribonucleoside QM data, the anti to high-anti region has been modified empirically. The reason is that subtle increase of the slope of the χ correction between the anti and high-anti regions as compared to the ff99 supports helical twist of B-DNA. It subtly increases the helical twist of B-DNA (see below) though it remains to be seen if this change can be significant for B-DNA modeling. However, the change is probably in the right direction.