Molecular Dynamics Simulation of an Allosteric Receptor by Simultaneous Casting and Molding in a Dynamic Combinatorial Library

Raw results of the molecular dynamics simulations performed for the paper:
<em>An Allosteric Receptor by Simultaneous Casting and Molding in a Dynamic Combinatorial Library</em>, J. Li, P. Nowak and S. Otto.
This fileset contains results of MD simulations on the macrocyclic isomer III (isoIII), gamma-cyclodextrin (CD), quaternary ammonium template (2) and complexes formed by them (CD-isoIII, isoIII-2, CD-isoIII-2). 
Files with the "structure_" prefix are snaphots from MD simulations at the time indicated in the filename.
Files with the ".traj" extension are Amber trajectory files (without water box) which can be loaded into a trajectory visualisation program (e.g. VMD, http://www.ks.uiuc.edu/Research/vmd/). The corresponding topology/parameter files have the ".prmtop" extension. The structures were saved every 10000 steps and the timestep was 2 fs. Therefore, in order to convert the frame number into simulation time, the former has to be multiplied by 1/50 ns. 
Files with the "distGAX-Y_" prefix contain the distances between the mass centers of glucopyranose residues X and Y of either free or complexed gamma-cyclodextrin as a function of simulation time.
Files with the "rmsfit" extension contain RMSD errors as a function of simulation time.
File "1BB.mol2" is the naphtalene fragment (from building block <strong>1</strong>) used to construct the isomer III macrocycle with the leap program. It was generated using restrained electrostatic fit (RESP) with RED.III.5 program. File "2TM" corresponds to the template <strong>2</strong> and was obtained the same way.