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 08:32:45 PDT 2020


Hi Carmen,

Sorry, I was looking at atoms 2, 3, and 4 in 3R1_pH74_netcharge.mol2. They are listed as:

       2 C1           2.1330    -2.3280     0.5080 ca            1 UNK        0.502600
       3 C2           1.3340    -1.2480     0.8230 ca            1 UNK       -0.458600
       4 C3           1.9460    -0.0180     0.9010 ca            1 UNK        0.698200

So the atom ids are fine (column 2) but the atom types are wrong (column 6). But you are right atom 9 as you stated:

       9 CA           5.9540     0.3730    -0.1620 c3            1 UNK        0.174500

has the correct atom type but is erroneously converted into a Calcium atom. The observations of the both of us agree that the 

	prepare_ligand4.py

script determines the atom type from the atom id and incorrectly ignores the atom type.

Fixing this problem by going by the atom type will break what the code does for atoms 2-4. However, in your examples it should be sufficient if the script checked the atom type when the atom id is ambiguous. Typical atom ids causing trouble are:

	CA
	CD
	CE
	CF (? I seem to remember this one but don't have an example for it right now)
	HO (occurs in Amber or Charmm , means Hydrogen attached to Oxygen, not Holmium)

I think these are the most common troublemakers.

Best wishes,

    Huub

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

On 9/4/20, 10:38, "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,


    Thank you for your reply.

    In the mol2, the atom named CA has the correct type c3 (and also the 3D structure is correct).


    9 CA           5.9540     0.3730    -0.1620 c3            1 UNK        0.174500


    The problem occurs only when I do the format conversion. In the pdbqt:


    ATOM     18 CA   UNK d   1       5.954   0.373  -0.162  0.00  0.00     0.174 Ca


    ...All other carbon atoms named C1, C2, C3... are correctly recognised.

    So far, I corrected this error manually by modifying the line above, i.e. adjust the spacing between 18 and CA and replace "Ca" with "Ca".


    ATOM     18  CA  UNK d   1       5.954   0.373  -0.162  0.00  0.00     0.174 C


    Anyway, I generated the mol2 file using the antechamber program from AmberTools20. After docking, I need to run MD simulations and this is why I parametrise the molecules in the first step. In this way, I can also use the same partial charges for docking.


    Best wishes,

    Carmen

    ________________________________
    From: autodock-bounces at scripps.edu <autodock-bounces at scripps.edu> on behalf of Van Dam, Hubertus <hvandam at bnl.gov>
    Sent: Friday, September 4, 2020 3:38:01 PM
    To: autodock at scripps.edu
    Subject: Re: ADL: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion

    Hi Carmen,

    Where did you get the mol2 files from? In MOL2 files (see: https://urldefense.com/v3/__http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTDBApG5Es$ ) 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: https://urldefense.com/v3/__http://tccc.iesl.forth.gr/education/local/quantum/molecular_modeling/guide_documents/SYBYL_data_document.html__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTDODoQzyQ$ ). 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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