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 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 (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.

 
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