Molecular Dynamics Information Extraction

Wednesday, April 9, 1997 - 10:45am - 11:45am
Keller 3-180
Denniis Sprous (Wesleyan University)
MD-trajectories currently span nanoseconds of simulated time. The parameters most commonly presented in MD papers are RMS, energy and temperature presented as functions of time. These are easily obtained from a variety of sources, most commonly the output files of the simulations itself. Most critical structural parameters are not available directly from program output files. Typically, these parameters are specific for a given molecule type. Pucker angle and other helicoidals are important for DNA. Ramachandran plots are obviously relevant for proteins. Hydrogen bond distances would be relevant for a ligand-DNA or ligand-protein simulation. The various modeling packages normally incorporate an analysis program such as the AMBER CARNAL program. The MD-ToolChest (MDTC) suite of programs was design to analyze data from a broad range of sources and can read trajectory files from AMBER, GROMOS and CHARMm. For DNA, its flagship program dials_and_windows_dna serves as a front end for passing coordinates to Lavery's Curves program. Complete helicoidal parameters are presented as time series. For proteins, a variety of torsional parameters will be analyzed and presented as graphs. AMBER4.1/PME simulations involving the Hagerman [1986, Nature 321, 449-450] sequences d[G5-{GA4T4C}2-C5] and d[G5-{GT4A4C}2-C5] are presented here to illustrate the process involved in using MDTC2.0 and Curves. Experimental evidence characterizes the d[GA4T4C]n as having a compressed minor groove and significant curvature. Conversely, d[GT4A4C]n lacks these features. MDTC provides utilities to determine RMS, to extract pdb files from AMBER trajectory files, and to view the complete set of DNA helicoidal parameters. Curves analysis is capable of returning measures of curvature and groove width, which are critical in comparing experiment to simulation. URL's will be referenced to provide access to example scripts. Joint work with Weidong Wang, Ganesan Ravishanker and David L. Beveridge.