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