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

Van Dam, Hubertus hvandam at bnl.gov
Fri Sep 4 06:38:01 PDT 2020


Hi Carmen,

Where did you get the mol2 files from? In MOL2 files (see: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf) the atom types are supposed to be SYBYL atom types. I guess the alpha-carbons should be sp3 carbons (in most cases?) which would be indicated with C.3 (see: http://tccc.iesl.forth.gr/education/local/quantum/molecular_modeling/guide_documents/SYBYL_data_document.html). The atom type ca is actually Calcium. So I think the script is converting the MOL2 files correctly as far as I can see, it is just that the MOL2 files don't specify the structure as it should. 

Best wishes,

    Huub

-----------------------------------------------------------------------------------------------------
Hubertus van Dam, 631-344-6020, hvandam at bnl.gov
Brookhaven National Laboratory
 

On 9/4/20, 04:59, "autodock-bounces at scripps.edu on behalf of Esposito  Carmen" <autodock-bounces at scripps.edu on behalf of carmen.esposito at phys.chem.ethz.ch> wrote:

    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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