ADL: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion

Esposito Carmen carmen.esposito at phys.chem.ethz.ch
Fri Sep 4 01:41:02 PDT 2020


Hi!

I am using the python script prepare_ligand4.py to convert mol2 files to pdbqt (I generate the mol2 files containing partial charges using antechamber of AmberTools20).

pythonsh prepare_ligand4.py -l file.mol2 -C -o file.pdbqt

However, I noticed that when doing the format conversion carbon atoms with the atom type CA (in the mol2) are transformed into calcium atoms (Ca, in the pdbqt file).
I attached here a couple of examples.
Is it possible that this is a bug?

Thank you very much for your help!

Best regards,
Carmen

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