8. solvate

This task is used to build a water box around the input molecule.

8.1. Arguments

-i, --in

Mandatory	Yes
Argument	PDB filename or XYZ filename
Default	None

Give the input molecule.

-t, --top

Mandatory	Yes
Argument	PSF filename
Default	None

Give the input topology.

-o, --out

Mandatory	No
Argument	A filename prefix
Default	None

Give the output filename prefix. If not given, the molecule and topology will be written to x-solvate.pdb and x-solvate.psf, respectively.

--box

Mandatory	Yes
Argument	Three real numbers: x, y, z in Angstrom
Default	None

Give the box size in Angstrom.

--charge

Mandatory	No
Argument	An integer.
Default	0

Give the target total charge of the system after adding ions. If not given, pdbtop will neutralize the system by adding counter ions (NaCl).

--ionic-strength

Mandatory	No
Argument	A real number in mol/L
Default	0.01

Give the target ionic strength of the system after adding ions. If not given, pdbtop will set the ionic strength to 0.01 mol/L by adding counter ions (NaCl).

--no-add-ions

Mandatory	No
Argument	None
Default	None

By default, pdbtop will add ions (NaCl) to the system. But if --no-add-ions is given, this will not be done.

--droplet

Mandatory	No
Argument	None
Default	None

If this is given, pdbtop will generate a droplet instead of box.

--move

Mandatory	No
Argument	Three real numbers: x, y, z in Angstrom
Default	None

Move the center of box or droplet size in Angstrom.

These are 2 examples:

# Solavte the system in a water box of 70x70x70 Angstrom^3 with default ionic strength (0.01 mol/L)
$ pdbtop.exe solvate -i 5vbm-92v-2.pdb -t 5vbm-92v-2.psf -o 5vbm-sol --box "70 70 70"

# Solavte the system in a water box of 70x70x70 Angstrom^3 with ionic strength 0.02 mol/L
$ pdbtop.exe solvate -i 5vbm-92v-2.pdb -t 5vbm-92v-2.psf -o 5vbm-sol --box "70 70 70" --ionic-strength 0.02