crd_convert
This program can manupulate trajectory data. For example, during the MD simulations, water molecules spread out from the unit cell, which can be wrapped into the unit cell by using crd_convert. In addition, the user can make a new trajectory file, where the focusing atoms are fitted to the initial structure, centered at the favorite position, and etc. Note that trajectory manipulation is done in the following order:
1) Centering
2) Wrapping
3) Fitting
To change this order, the users should modify the source codes in cc_convert.fpp in crd_convert by themselves.
This program can also convert the DCD format to PDB format. If the user specify split_trjpdb = YES, all snapshots in the trajectory files are split into individual PDB files.
Target protein is centered at the origin, and water and ions are wrapped into the unit cell
[INPUT] psffile = ../BPTI_ionize.psf # protein structure file reffile = ../BPTI_ionize.pdb # PDB file [OUTPUT] trjfile = output.dcd # trajectory 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 = all # select all atoms group2 = segid:BPTI # select protein atoms [FITTING] fitting_method = NO # [NO,TR,TR+ROT,TR+ZROT,XYTR,XYTR+ZROT] [OPTION] check_only = NO trjout_format = DCD # write DCD format trjout_type = COOR+BOX trjout_atom = 1 # output all atoms split_trjpdb = NO centering = YES # protein is centered at the origin centering_atom = 2 center_coord = 0.0 0.0 0.0 pbc_correct = MOLECULE # molecules are wrapped into the unit cell
Make a new DCD file that contain only CA atoms of the protein (no fitting and no centering)
[SELECTION] group1 = an:CA and segid:BPTI # select protein CA atoms [FITTING] fitting_method = NO # [NO,TR,TR+ROT,TR+ZROT,XYTR,XYTR+ZROT] [OPTION] check_only = NO trjout_format = DCD # write DCD format trjout_type = COOR+BOX trjout_atom = 1 # output all atoms split_trjpdb = NO centering = NO # protein is centered at the origin pbc_correct = NO
Make a new DCD file that contain only protein CA atoms with fitting to the initial coordinates
[SELECTION] group1 = an:CA and segid:BPTI # select protein CA atoms [FITTING] fitting_method = TR+ROT # [NO,TR,TR+ROT,TR+ZROT,XYTR,XYTR+ZROT] fitting_atom = 1 [OPTION] check_only = NO trjout_format = DCD # write DCD format trjout_type = COOR+BOX trjout_atom = 1 # output all atoms split_trjpdb = NO centering = NO # protein is centered at the origin pbc_correct = NO
Combine several dcd files into one dcd file
See also this page.
[INPUT] psffile = ../BPTI_ionize.psf # protein structure file reffile = ../BPTI_ionize.pdb # PDB file [OUTPUT] trjfile = output.dcd # trajectory file [TRAJECTORY] trjfile1 = ../BPTI_run1.dcd # trajectory file trjfile2 = ../BPTI_run2.dcd # trajectory file trjfile3 = ../BPTI_run3.dcd # trajectory file trjfile4 = ../BPTI_run4.dcd # trajectory file trjfile5 = ../BPTI_run5.dcd # trajectory file md_step1 = 500000 # number of MD steps mdout_period1 = 500 # MD output period ana_period1 = 500 # analysis period repeat1 = 5 trj_format = DCD # (PDB/DCD) trj_type = COOR+BOX # (COOR/COOR+BOX) trj_natom = 0 # (0:uses reference PDB atom count) [SELECTION] group1 = all # select all atoms [FITTING] fitting_method = NO # [NO,TR,TR+ROT,TR+ZROT,XYTR,XYTR+ZROT] [OPTION] check_only = NO trjout_format = DCD # write DCD format trjout_type = COOR+BOX trjout_atom = 1 # output all atoms
Split coordinates trajectory data into individual PDB file
[INPUT] psffile = ../BPTI_ionize.psf # protein structure file reffile = ../BPTI_ionize.pdb # PDB file [OUTPUT] trjfile = output{}.pdb # trajectory 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 = all # select all atoms group2 = segid:BPTI # select protein atoms [FITTING] fitting_method = NO # [NO,TR,TR+ROT,TR+ZROT,XYTR,XYTR+ZROT] [OPTION] check_only = NO trjout_format = PDB # write PDB trjout_type = COOR+BOX trjout_atom = 1 # output all atoms split_trjpdb = YES centering = YES # protein is centered at the origin centering_atom = 2 center_coord = 0.0 0.0 0.0 pbc_correct = MOLECULE # molecules are wrapped into the unit cell