2. remove

In this task, pdbtop will remove ions, waters, ligands, chains, etc. from the input molecule.

Hint

All removing operations are done by residue. To delete a single atom, please refer to modify.

2.1. Arguments

-i, --in

Mandatory	Yes
Argument	PDB filename or XYZ filename
Default	None

Give the input molecule.

-o, --out

Mandatory	No
Argument	A filename prefix
Default	None

Give the output filename prefix. If not given, the output will be written to x-remove.pdb.

--ions

Mandatory	No
Default	False

Remove ions from the input molecule, like Na⁺, Cl^-, SO₄^2-, etc.

--waters

Mandatory	No
Default	False

Remove waters from the input molecule.

--ligands

Mandatory	No
Default	False

Remove ligands from the input molecule.

Example:

$ # Remove ions, waters, and ligands from the input molecule
$ pdbtop remove -i 3kab.pdb --ions --waters --ligands -o 3kab-protein.pdb

--chains

Mandatory	No
Argument	1 or more chain IDs, like A or "B C"
Default	False

Remove chains from the input molecule.

Example:

$ pdbtop remove -i 3kab.pdb --chains "A B" # Remove chain A and B from the input molecule
$ pdbtop remove -i 3kab.pdb --chains A     # Remove chain A from the input molecule