rmsd_analysis
In usual, we analyze RMSD of the protein Calpha atoms with respect to the initial structure as in Ex1. reffile in [INPUT] is the reference coordinates. We can also specify fitting atoms and analysis atoms separately. For example, RMSD of the ligand with respect to the protein can be analyzed (see Ex2).
Ex1) RMSD with respect to the protein Calpha atoms in the initial structure
[INPUT] psffile = ../BPTI_ionize.psf # protein structure file reffile = ../BPTI_ionize.pdb # PDB file [OUTPUT] rmsfile = output.rms # RMSD file [TRAJECTORY] trjfile1 = ../BPTI_run.dcd # trajectory file md_step1 = 500000 # number of MD steps mdout_period1 = 500 # MD output period ana_period1 = 500 # analysis period repeat1 = 1 trj_format = DCD # (PDB/DCD) trj_type = COOR+BOX # (COOR/COOR+BOX) trj_natom = 0 # (0:uses reference PDB atom count) [SELECTION] group1 = an:CA # selection group 1 [FITTING] fitting_method = TR+ROT # [NO,TR,TR+ROT,TR+ZROT,XYTR,XYTR+ZROT] fitting_atom = 1 # atom group mass_weight = NO # mass-weight is not applied [OPTION] check_only = NO # (YES/NO) analysis_atom = 1 # atom group
Ex2) RMSD of the ligand by fitting protein Calpha atoms
[INPUT] psffile = ../protein_atp.psf # protein structure file reffile = ../protein_atp.pdb # PDB file [OUTPUT] rmsfile = output.rms # RMSD file [TRAJECTORY] trjfile1 = ../protein_atp.dcd # trajectory file md_step1 = 500000 # number of MD steps mdout_period1 = 500 # MD output period ana_period1 = 500 # analysis period repeat1 = 1 trj_format = DCD # (PDB/DCD) trj_type = COOR+BOX # (COOR/COOR+BOX) trj_natom = 0 # (0:uses reference PDB atom count) [SELECTION] group1 = an:CA # selection group 1 group2 = rnam:ATP [FITTING] fitting_method = TR+ROT # [NO,TR,TR+ROT,TR+ZROT,XYTR,XYTR+ZROT] fitting_atom = 1 # atom group mass_weight = NO # mass-weight is not applied [OPTION] check_only = NO # (YES/NO) analysis_atom = 2 # atom group