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@article{1356111, author = {GalindoandMurillo, Rodrigo and Robertson, James C. and Zgarbová, Marie and Šponer, Jiří and Otyepka, Michal and Jurečka, Petr and Cheatham, Thomas E.}, article_location = {Washington DC}, article_number = {8}, doi = {http://dx.doi.org/10.1021/acs.jctc.6b00186}, keywords = {MOLECULAR-DYNAMICS SIMULATIONS; PARTICLE MESH EWALD; PAIR OPENING KINETICS; IMINO PROTON-EXCHANGE; B-DNA; NUCLEIC-ACIDS; BIOMOLECULAR SIMULATIONS; SYNTHETIC DNA; RNA; DODECAMER}, language = {eng}, issn = {1549-9618}, journal = {Journal of Chemical Theory and Computation}, title = {Assessing the Current State of Amber Force Field Modifications for DNA}, url = {http://pubs.acs.org/doi/pdf/10.1021/acs.jctc.6b00186}, volume = {12}, year = {2016} }
TY - JOUR ID - 1356111 AU - Galindo-Murillo, Rodrigo - Robertson, James C. - Zgarbová, Marie - Šponer, Jiří - Otyepka, Michal - Jurečka, Petr - Cheatham, Thomas E. PY - 2016 TI - Assessing the Current State of Amber Force Field Modifications for DNA JF - Journal of Chemical Theory and Computation VL - 12 IS - 8 SP - 4114-4127 EP - 4114-4127 PB - American Chemical Society SN - 15499618 KW - MOLECULAR-DYNAMICS SIMULATIONS KW - PARTICLE MESH EWALD KW - PAIR OPENING KINETICS KW - IMINO PROTON-EXCHANGE KW - B-DNA KW - NUCLEIC-ACIDS KW - BIOMOLECULAR SIMULATIONS KW - SYNTHETIC DNA KW - RNA KW - DODECAMER UR - http://pubs.acs.org/doi/pdf/10.1021/acs.jctc.6b00186 L2 - http://pubs.acs.org/doi/pdf/10.1021/acs.jctc.6b00186 N2 - The utility of molecular dynamics (MD) simulations to model biomolecular structure, dynamics, and interactions has witnessed enormous advances in recent years due to the availability of optimized MD software and access to significant computational power, including GPU multicore computing engines and other specialized hardware. This has led researchers to routinely extend conformational sampling times to the microsecond level and beyond. The extended sampling time has allowed the community not only to converge conformational ensembles through complete sampling but also to discover deficiencies and overcome problems with the force fields. Accuracy of the force fields is a key component, along with sampling, toward being able to generate accurate and stable structures of biopolymers. The Amber force field for nucleic acids has been used extensively since the 1990s, and multiple artifacts have been discovered, corrected, and reassessed by different research groups. We present a direct comparison of two of the most recent and state-of-the-art Amber force field modifications, bsc1 and OL15, that focus on accurate modeling of double-stranded DNA. After extensive MD simulations with five test cases and two different water models, we conclude that both modifications are a remarkable improvement over the previous bsc0 force field. Both force field modifications show better agreement when compared to experimental structures. To ensure convergence, the Drew-Dickerson dodecamer (DDD) system was simulated using 100 independent MD simulations, each extended to at least 10 mu s, and the independent MD simulations were concatenated into a single 1 ms long trajectory for each combination of force field and water model. This is significantly beyond the time scale needed to converge the conformational ensemble of the internal portions of a DNA helix absent internal base pair opening. Considering all of the simulations discussed in the current work, the MD simulations performed to assess and validate the current force fields and water models aggregate over 14 ms of simulation time. The results suggest that both the bsc1 and OL15 force fields render average structures that deviate significantly less than 1 angstrom from the average experimental structures. This can be compared to similar but less exhaustive simulations with the CHARMM 36 force field that aggregate to the similar to 90 mu s time scale and also perform well but do not produce structures as close to the DDD NMR average structures (with root-mean-square deviations of 1.3 angstrom) as the newer Amber force fields. On the basis of these analyses, any future research involving double-stranded DNA simulations using the Amber force fields should employ the bsc1 or OL15 modification. ER -
GALINDO-MURILLO, Rodrigo, James C. ROBERTSON, Marie ZGARBOVÁ, Jiří ŠPONER, Michal OTYEPKA, Petr JUREČKA a Thomas E. CHEATHAM. Assessing the Current State of Amber Force Field Modifications for DNA. \textit{Journal of Chemical Theory and Computation}. Washington DC: American Chemical Society, 2016, roč.~12, č.~8, s.~4114-4127. ISSN~1549-9618. Dostupné z: https://dx.doi.org/10.1021/acs.jctc.6b00186.
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