drms_analysis
drms_analysis is a tool calculating distance RMS (dRMS) from structure(s).
# example dRMS of inter domains (group1 and group3) [INPUT] psffile = psf pdbfile = open.pdb reffile = close.pdb [OUTPUT] rmsfile = drms.log # log file [TRAJECTORY] trjfile1 = pr.1.pdb # trajectory file md_step1 = 1 # number of MD steps mdout_period1 = 1 # MD output period ana_period1 = 1 # analysis period repeat1 = 1 trj_format = PDB # (PDB/DCD) trj_type = COOR # (COOR/COOR+BOX) trj_natom = 0 # (0:uses reference PDB atom count) [SELECTION] group1 = (resno:1-29) or (resno:68-117) or (resno:161-214) group2 = (resno:30-67) group3 = (resno:118-167) [OPTION] check_only = NO # (YES/NO) contact_groups = 1 3 #main-NMP minimum_distance = 6.0 maximum_distance = 10.0 avoid_bonding = yes exclude_residues = 0