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Article ID: 1091 - Last Modified:

What structure file formats can be used with the LigPrep package?

LigPrep itself reads Maestro, MDL SD (.sd or .sdf), and SMILES formatted files, and writes Maestro and SD files.

Maestro has the ability to read and write files in the following formats:

  • MacroModel*
  • Maestro*
  • PDB*
  • Sybyl Mol2*
  • MDL SD (.mol)*
  • Jaguar input
  • Many formats supported by Babel

Additional utilities supplied with all Schrödinger products permit separate conversion of the asterisked formats.

LigPrep does not read PDB files, because raw PDB structures do not have explicit multiple bonds and formal charges.

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