flccrd_analysis
flccrd_anslysis compute the RMSF (Root-mean-square fluctuation) of the selected atoms. This tool is also used for the principal component analysis (PCA). See Tutorials 2.1.5.5 and 4.4. In the case of “vcv_matrix = Global” analysis_atoms are analyzed, while in the case of “vcv_matrix = Local” fitting_atoms are analyzed.
Calculation of the RMSF of the protein CA atoms
[INPUT]
reffile = 2ech.pdb # PDB file
psffile = 2ech.psf # PSF file
pdb_avefile = ../1_avecrd/output_ave.pdb # PDB file obtained by avecrd_analysis
pdb_aftfile = ../1_avecrd/output_aft.pdb # PDB file obtained by avecrd_analysis
[OUTPUT]
pcafile = output.pca # PCA file
rmsfile = output.rms # RMSF file
vcvfile = output.vcv # Variance-Covarience Matrix file
crsfile = output.crs # CRS file
[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)
vcv_matrix = Global # (GLOBAL/LOCAL)
analysis_atom = 1 # analysis target atom group