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 07:21:44 PDT 2020


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: 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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