Command line options and parameters
SOLVATE receives all input parameters from the command line, so it can easily be used within shell-scripts.
Available options are:
solvate [-t thick] [-r radius] [-n ngauss] [-ug] [-ub]
[-s] [-v] [-bulk] [-w] [-ion] [-q charge] [-psf] [infile] outfile
thick
specifies the minimum water shell thickness in Angstrom (default: 10.0). Nowhere will the solute be closer to the surface of the solvent than this value. Attention: Values smaller than 3.0 may confuse SOLVATE.
radius
specifies the maximum boundary curvature radius of the solvent surface in Angstrom (default: 100000.0). A very large value (e.g., the default value) means that the surface can (but not necessarily does) have rather flat parts. Smaller values generate `rounder' solvent volumes, and, as a consequence, more solvent molecules. The value of radius should not be considerably smaller than the size of the solute.
ngauss
specifies the number of gaussians to be used to define the solvent surface (default: 1). The more detailed irregular features of the surface are required, the more gaussians should be used. Consequently, thin water shells typically require more gaussians than thicker ones. Note, however, that a large number may slow down subsequent molecular dynamics simulations. Typical values for ngauss are five to ten.
-s
If the -s option is set, the file surface_stat is written, which contains (i) a set of grid points specifying the solvent surface, (ii) the error statistics for the distance estimate described above, and (iii) information about how many water molecules belong to which group of molecules.
-v
If the -v option is set, the file volume_stat is written (attention: this file may become quite large!), which lists for every grid point within the solvent volume its x-, y-, and z-coordinate, the value f(x, y, z) of the density function at this point, its accurate distance and the approximate distance (which is the efficient estimate used in subsequent MD-simulations) from the solute surface, as well as an approximate value of the curvature of the surface at the point next to (x, y, z) (which also is an efficient estimate that can be used in MD-simulations).
-ug
If the -ug (use gaussians) option is set, all steps required for the computation of the approximate density function f (STEPs 2 and 3) are skipped, and the required parameters for defining f are read from the file gaussians.lis instead, which is always written when f is computed. The reason for this option is that STEP 3 is quite time consuming.
-ub
If the -ub (use boundary) option is set, all steps required for the computation of the boundary description through f (STEPs 2, 3, and 4) are skipped, and the required parameters for defining f and the scale factor s are read from the file boundary.lis instead, which is always written after the boundary distance from the solute has been adjusted (STEP 4). The reason for this option is that STEP 4 is quite time consuming.
-bulk
The -bulk option suppresses output of buried water molecules, i.e., only bulk water is written to the output pdb-file.
-w
The -w option suppresses output of the solute, i.e., only water molecules (usually with a hole in the middle, where the solute is located) and ions are written to the output pdb-file.
-ion
If the -ion option is set, STEP 9 is carried out to place sodium and chloride ions into the solvent according to a isotonic Debye-Hückel density. If the option is not given, STEP 9 is skipped, and no ions are output.
-q charge
Use this option in addition to -ion to control the total charge of the output system. -q 0 will produce a neutral system.
-psf
If the -psf option is set, SOLVATE writes an X-PLOR-script mkpsf.inp" which can be used to generate a structure file for the solute/solvent-system, as required for subsequent MD-simulations (the command xplor < mkpsf.inp will do the job).
infile
specifies the name of the input pdb-/psf-file of the solute. If the -ion option is set, both pdb- and psf-file are required;otherwise only the pdb-file is needed. No extension must be given! The input file name may be omitted, in which case SOLVATE creates a pure spherical water droplet centered at the origin.
outfile
specifies the name of the output file for the solute/solvent-system. No extension should be given. The command line options can be given in arbitrary sequence.