6. pdb

This task is used to obtain a better PDB file. Here “better” meansing correct atom names, residue names, etc., and coordinates into a PBC box.

6.1. Arguments

-i, --in

Mandatory	Yes
Argument	PDB filename or XYZ filename
Default	None

Give the input molecule.

-t, --top

Mandatory	No
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 will be written to x-pdb.pdb.

--box

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

The box size in Angstrom. If given, all coordinates will be moved into this box. A residue will NOT be split into two parts.

Here is an example:

$ pdbtop.exe pdb -i mol.xyz -t mol.psf -o mol-sol --box "70 70 70"

The output mol-sol.pdb will contain coordinates given in mol.xyz and topology given in mol.psf. The coordinates will be moved into a box with size 70x70x70 Angstrom, shown below.