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Article ID: 435 - Last Modified:

How can I correct some AMBER-generated PDB files and make them format-compliant and readable by Maestro?

It is possible to convert the PDB file into a format that complies with official PDB standard using some manual editing and OpenBabel (

To fix such structures, the important changes that have to be made by hand are:

1) Change ATOM records to HETATM for all non-protein atoms
2) Change WAT residue name to HOH for all waters

The rest of the changes (such as deleting unnecessary TER records) and making the structure fully compliant with the official PDB format can done by processing it with OpenBabel.

Keywords: convert, standard PDB , openbabel, AMBER , Maestro

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