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Solvator(1) Manual Page

Name

Solvator - Creates a box of solvent around a solute.

Synopsis

Solvator [-hrVx] [--abc=a,b,c] [-b=2.5] [--iFi=ions] [-p=9.0] [-s=auto] [--sFi=water] file

Description

Creates a box of solvent around a solute.

Options

--abc, --boxLengths=a,b,c

Specify a comma-separated set of unit cell box lengths, instead of calculating them (a,b,c)

-b, --boundary=2.5

Delete solvent molecules that infringe closer than this to the solute.

-h, --help

Print command help and exit.

--iFi, --ionFile=ions

Name of the file containing ions. Must also have a .ions file (e.g. nacl.pdb must also have nacl.ions). Default: no ions.

-p, --padding=9.0

Sets the minimum amount of solvent padding around the solute.

-r, --rectangular

Use a rectangular prism rather than a cube for solvation.

-s, --randomSeed=auto

Specify a random seed for ion placement.

--sFi, --solventFile=water

A file containing the solvent box to be used. There is currently no default.

-V, --version

Print the Force Field X version and exit.

-x, --translate

Move solute molecules to center of box. Turning off should only considered when specifying the unit cell box dimensions

Arguments

file

The atomic coordinate file in PDB or XYZ format.