AutoDock PDBQT format (pdbqt)

Reads and writes AutoDock PDBQT (Protein Data Bank, Partial Charge (Q), & Atom Type (T)) format

Note that the torsion tree is by default. Use the r write option to prevent this.

Read Options

-b

Disable automatic bonding

-d

Input file is in dlg (AutoDock docking log) format

Write Options

-b

Enable automatic bonding

-r

Output as a rigid molecule (i.e. no branches or torsion tree)

-c

Combine separate molecular pieces of input into a single rigid molecule (requires “r” option or will have no effect)

-s

Output as a flexible residue

-p

Preserve atom indices from input file (default is to renumber atoms sequentially)

-h

Preserve hydrogens

-n

Preserve atom names