This tool calculates a spatial density distribution of ‘solvent’ atoms around ‘solute’ atoms from input trajectory files. It is better for density calculation if the trajectory was simulated in constant volume condition (i.e. NVT or NVE condition).
It computes electron density distribution (
ELECTRON) or simply number density distribution (
ELECTRON, this tool computes the average number of electrons (q = the atomic number – the partial charge) of ‘solvent’ atoms visiting each voxel:
(i: snapshot number, Nsnapshot: total number of snapshots used in the calculation,
The atomic number of each atom is calculated from atom_type written in a psf/prmtop file. You can check these values used in analyses by viewing a log file when you set
number, the tool computes simply the average of the number of times that ‘solvent’ atoms visited in each voxel:
ρN(x, y, z) = Σi (δ (x, y, z)) / Nsnapshot
(δ: if a solvent atom visits the voxel in a snapshot, δ =1; otherwise δ = 0)
The calculated spatial density distribution is output in any of the three formats: CCP4, XPLOR/CNS and OpenDX. Molecular visualization programs like PyMOL ,VMD support these file formats. CCP4mg program also supports ccp4-format density file whose extension is “.map”. The output file format is specified by
output_format in [DENSITY_OPTION]. The resolution of the output density distribution is specified by ‘
voxel_size‘ (the unit is Å).
The box dimensions used for the density distribution calculation are the box dimensions of the simulation box when
MANUAL, the box dimensions used for the distribution calculation is equal to the values of box_size_[x, y, z] in [BOUNDARY] section. In this case, the center of the box for the density output is the center of the mass of the ‘solute’ molecule. In Both cases, the cutoff (the thickness of the buffer region) length Δr should be larger than the range used for the distribution calculation d.
Finally, when a calculated density distribution is output, the box dimensions are shrank to include only voxels where density values are non-zero.
This tool has functions to center a target molecule of interest (
recenter), to wrap solvent molecules (
wrap) and to superimpose the molecule to a reference molecule (
fitting_method). Thus you do not need to run any programs such as ‘
crd_convert‘ before you use this tool.
[INPUT] psffile = BPTI_solvate.psf reffile = BPTI_solvate.pdb pdbfile = BPTI_solvate.pdb [OUTPUT] mapfile = BPTI_hydration.ccp4 # file name for the 3D-distribution output pdbfile = BPTI_density.pdb # please use this file when you view the 3D density together with the reference structure. [TRAJECTORY] trjfile1 = run.dcd md_step1 = 1000 mdout_period1 = 1 ana_period1 = 1 trj_format = DCD trj_type = COOR+BOX [BOUNDARY] type = PBC domain_x = 2 domain_y = 2 domain_z = 2 num_cells_x = 70 num_cells_y = 70 num_cells_z = 70 [ENSEMBLE] ensemble = NVE # NVT or NVE ensemble is recommended [SELECTION] group1 = resno:1-58 & an:CA group2 = resname:TIP3 group3 = resno:1-58 [FITTING] fitting_method = TR+ROT fitting_atom = 1 mass_weight = NO [SPANA_OPTION] wrap = yes buffer = 10.0 box_size = TRAJECTORY # (TRAJECTORY / MANUAL / MAX) [DENSITY_OPTION] density_type = ELECTRON # (ELECTRON / NUMBER) output_format = CCP4 # (CCP4 / XPLOR / DX) verbose = no # if yes, # partial charge and atomic number of each atom is output in log file solute = 3 solvent = 2 recenter = 1 range = 8.0 # calculation range around solute atom voxel_size = 1.0 # resolution of the output density # magnification = 6.0 # useful when you view the output density distribution using PyMOL software