avecrd_analysis
This tool is also used for the principal component analysis (PCA). See Tutorials 2.1.5.5 and 4.4.
Calculation of the averaged coordinates of the protein CA atoms
[INPUT] reffile = 2ech.pdb # PDB file psffile = 2ech.psf # PSF file [OUTPUT] pdbfile = output.pdb # Coordinates of reference structure rmsfile = output.rms # RMSD with respect to the average pdb_avefile = output_ave.pdb # Averaged coordinates of analysis atoms pdb_aftfile = output_aft.pdb # Averaged coordinates of fitting atoms [TRAJECTORY] trjfile1 = md.dcd # trajectory file md_step1 = 5000 # number of MD steps mdout_period1 = 1 # MD output period ana_period1 = 1 # 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) num_iterations = 10 # number of iterations analysis_atom = 1 # analysis target atom group