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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.
