Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules Export

@article{citeulike:2099003, abstract = {An explicit ion, implicit water solvent model for molecular dynamics was developed and tested with DNA and RNA simulations. The implicit water model uses the finite difference Poisson (FDP) model with the smooth permittivity method implemented in the OpenEye ZAP libraries. Explicit counter-ions, co-ions, and nucleic acid were treated with a Langevin dynamics molecular dynamics algorithm. Ion electrostatics is treated within the FDP model when close to the solute, and by the Coulombic model when far from the solute. The two zone model reduces computation time, but retains an accurate treatment of the ion atmosphere electrostatics near the solute. Ion compositions can be set to reproduce specific ionic strengths. The entire ion/water treatment is interfaced with the molecular dynamics package CHARMM. Using the CHARMM-ZAPI software combination, the implicit solvent model was tested on A and B form duplex DNA, and tetraloop RNA, producing stable simulations with structures remaining close to experiment. The model also reproduced the A to B duplex DNA transition. The effect of ionic strength, and the structure of the counterion atmosphere around B form duplex DNA were also examined. {\copyright} 2007 Wiley Periodicals, Inc. J Comput Chem, 2008}, address = {Schering-Plough, Kenilworth, NJ, USA; Astra-Zeneca, Bangalore, India; Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania 19104}, author = {Prabhu, Ninad V. and Panda, Manoranjan and Yang, Qingyi and Sharp, Kim A.}, citeulike-article-id = {2099003}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/jcc.20874}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18074338}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18074338}, citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/117861682/ABSTRACT}, doi = {10.1002/jcc.20874}, issn = {1096-987X}, journal = {Journal of Computational Chemistry}, keywords = {implicit\_solvation, md\_dna, molecular\_dynamics}, number = {7}, pages = {1113--1130}, posted-at = {2008-03-09 01:52:28}, priority = {2}, title = {Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules}, url = {http://dx.doi.org/10.1002/jcc.20874}, volume = {29}, year = {2008} }

TY - JOUR ID - citeulike:2099003 L3 - citeulike-article-id:2099003 N2 - An explicit ion, implicit water solvent model for molecular dynamics was developed and tested with DNA and RNA simulations. The implicit water model uses the finite difference Poisson (FDP) model with the smooth permittivity method implemented in the OpenEye ZAP libraries. Explicit counter-ions, co-ions, and nucleic acid were treated with a Langevin dynamics molecular dynamics algorithm. Ion electrostatics is treated within the FDP model when close to the solute, and by the Coulombic model when far from the solute. The two zone model reduces computation time, but retains an accurate treatment of the ion atmosphere electrostatics near the solute. Ion compositions can be set to reproduce specific ionic strengths. The entire ion/water treatment is interfaced with the molecular dynamics package CHARMM. Using the CHARMM-ZAPI software combination, the implicit solvent model was tested on A and B form duplex DNA, and tetraloop RNA, producing stable simulations with structures remaining close to experiment. The model also reproduced the A to B duplex DNA transition. The effect of ionic strength, and the structure of the counterion atmosphere around B form duplex DNA were also examined. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 IS - 7 JF - Journal of Computational Chemistry SN - 1096-987X AD - Schering-Plough, Kenilworth, NJ, USA; Astra-Zeneca, Bangalore, India; Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania 19104 EP - 1130 TI - Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules VL - 29 SP - 1113 KW - implicit_solvation KW - md_dna KW - molecular_dynamics AU - Prabhu, Ninad AU - Panda, Manoranjan AU - Yang, Qingyi AU - Sharp, Kim PY - 2008/// UR - http://dx.doi.org/10.1002/jcc.20874 ER -