Dash clustering and NOE dist analysis of SAM MDs

Collection of MD analysis scripts for cluster analysis and distance analysis: running amberdash:amberdash uses the commandline provided amberdash.inptext. It needs the information about the dihedral angles to be clustered (seed.tor) the MD trajectories used (seed.trajin) and a corresponding toppology file for the MD (seed.trj). dashstate-trajectories.pl:Script creates and runs cpptraj input that reads original MD trajectories and dash.out to create first multiple short dashstate trajectory files which are combined into Dihedcluster[n].trj files containing all structures per cluster. analyseDihedclusters.pl:uses ptraj to read individual Dihedcluster[n].trj trajectory files and calculates rmsd, partial rmsd, defined dihedral angles, individual distances, averaged distances, r^-6 averaged distances and their histograms and standard deviations. In this example this is printed into several files including a summary file for the ditance analysis used for NOE fitting afterwards.