3. topol

This task is used to add missing atoms and build the topology of the input molecule.

Hint

It is strongly recommended to use check to correct the molecules before generating topology.

3.1. 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 molecule and topology will be written to x-topol.pdb and x-topol.psf, respectively.

Example:

# Add hydrogen atoms, then build the topology.
$ pdbtop topol -i 3kab-protein.pdb -o 3kab-topol

--add-rtfs

Mandatory	No
Argument	Additional residue topology files.
Default	None

Give additional residue topology files (RTF), path can be included.

By default, pdbtop will load RTF files in data/. If you want to add your own ones, you can use this option.

Example:

# Add 2 topology files: ``my-topology1.rtf`` and ``/usr/data/my-topology2.rtf``.
$ pdbtop topol -i 3kab-protein.pdb -o 3kab-topol --add-rtfs "my-topology1.rtf /usr/data/my-topology2.rtf"

--no-patching-terminus

Mandatory	No
Default	False

By defulat, pdbtop will add N- and C-terminus for each protein chain. But if --no-patching-terminus is given, this will not be done.

Hint

It you want to do some modifications on the terminal resiudes, you’d better use --no-patching-terminus at this stage. After modifications, you can patch terminus again.