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Amber Prep format (prep)

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DL-POLY CONFIG (CONFIG)

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Autodock Protein Data Bank (pdbqt)

Q (Partial Charge) & Type

Read Options

b Disable automatic bonding
d Input file is in dlg (docking log file) format.

Write Options

b Enables automatic bonding before writing to pdbqt format
r Outputs rigid molecule (no branches)
s Outputs as a flexible residue
p

Preserves the atom indexes from the input file

The default is to renumber sequentially.