4. modify

This task is used to modify the residues of the input molecule.

4.1. 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-modify.pdb and x-modify.psf, respectively.

--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"

Modifications

In the following table, the modifications are listed.

--mml	Mono-Methyl-Lysine	Lysine
--dml	Di-Methyl-Lysine	Lysine
--tml	Tri-Methyl-Lysine	Lysine
--mma	Mono-Methyl-Arginine	Arginine
--adma	Asymmetric Di-Methyl-Arginine	Arginine
--sdma	Symmetric Di-Methyl-Arginine	Arginine
--pho	Phosphorylation	Serine, Threonine, Tyrosine
--my-mod	User-defined modification	Any residue

For --my-mod, please refer to Tutorial 6: Define My Own Modification, which shows how to define your own modification.

--mutate

:stub-columns: 1

Mandatory	No
Argument	A set of mutations, like “17A SER 34A ALA”
Default	None

Mutate a residue to another one.

Example:

# Mutate residue 17 at chain A (which is an arginine) to serine.
$ pdbtop modify -i 3kab.pdb -t 3kab.psf -o 3kab-R17S --mutate "17A SER"
# Do 2 mutations.
$ pdbtop modify -i 3kab.pdb -t 3kab.psf -o 3kab-M2 --mutate "17A SER 34A ALA"

--add-bonds

Mandatory	No
Argument	A set of bonds, like “12 45 409 230”
Default	None

Add additional bonds.

Example:

# Add 2 bonds: 12-45, 409-230.
$ pdbtop modify -i 3kab.pdb -t 3kab.psf --add-bonds "12 45 409 230" -o 3kab-cov

Hint

All atom indices starts from 1.

--del-atom

Mandatory	No
Argument	An atom, like 12
Default	None

Delete an atom.

Example:

# Add the 23rd atom.
$ pdbtop modify -i 3kab.pdb -t 3kab.psf --del-atom 23 -o 3kab-del

All modifictions are done in place and can be combined. For example:

$ pdbtop modify -i 3kab.pdb -t 3kab.psf --del-atom 23 --add-bonds "12 45" --mutate "17A SER" -o 3kab-mod

However, if you do modifications for the same residue, the result may be unpredictable. You must carefully examine if the result is right!

# The 154th atom is in residue 17 at chain A. So, doing them together may cause problems.
$ pdbtop modify -i 3kab.pdb -t 3kab.psf --del-atom 154 --mutate "17A SER" -o 3kab-mod