Solvator(1) Manual Page

Name

Solvator - Creates a box of solvent around a solute.

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

Creates a box of solvent around a solute.

--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