Predicting RNA Structures via a Simple van der Waals Correction to an All-Atom Force Field

• DOI: 10.1021/acs.jctc.6b00808
• Publication Date: 2016-12-29T17:07:40Z
• Authors: Changwon Yang; Manho Lim; Eunae Kim; Youngshang Pak
• Keywords: 01 natural sciences; 0104 chemical sciences

We proposed a simple van der Waals backbone correction (O2' and OP) to the AMBER ff12 force field in conjunction with the OPC water via an unequal Lorentz-Berthelot combination rule. As tested on four different tetranuceotides such as r(GACC), r(CCCC), r(AAAA), and r(CAAU), this new force field correctly captured each native fold as the largest population. For a RNA tetraloop (UUCG) tested, the stability of its native fold is substantially improved.