[AMBER] Fw: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion

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From: Esposito Carmen <carmen.esposito.phys.chem.ethz.ch>
Date: Wed, 2 Sep 2020 13:17:09 +0000

Dear developers,

I am using AmberTools20 to parametrize small molecules and generate pdbqt files.

I have used antechamber to generate the partial charges and the python script prepare_ligand4.py to convert the mol2 file to pdbqt.

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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application/octet-stream attachment: 3R1_pH74_netcharge.mol2

application/octet-stream attachment: 3R1_pH74_netcharge.pdbqt

application/octet-stream attachment: CKO_pH74_netcharge.mol2

application/octet-stream attachment: CKO_pH74_netcharge.pdbqt

Received on Wed Sep 02 2020 - 06:30:07 PDT