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

From: Esposito Carmen <>
Date: Fri, 4 Sep 2020 08:26:43 +0000

Hi Charo,

Thank you for your suggestions.

I am using AmberTools20 to parameterize the compounds because then I need to run a MD simulation afterward.

I do not know Avogadro2 but usually, I use a combination of RDKit and ChemAxon to prepare the molecules and determine protonation and tautomeric states. I will have a look at Avogadro.

I am using Autodock Vina, but thank you for your comment!


From: Charo del Genio <>
Sent: Friday, September 4, 2020 10:17:31 AM
To: AMBER Mailing List; Esposito Carmen
Subject: Re: [AMBER] Fw: converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion

On 02/09/2020 14:17, Esposito Carmen wrote:
> 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 to convert the mol2 file to pdbqt.
> pythonsh -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

Dear Carmen,
        I have a couple of suggestions and comments for you, if I may.

First, why are you using Amber to prepare molecules for docking? Docking is an inherently much less precise method than MD, so using Amber to prepare molecules for Autodock is a massive overkill. My
operative suggestion is as follows:

1) Draw your molecules using Avogadro2 (which is the successor to the good old Avogadro).
2) From within the interface of Avogadro2, minimize the configuration of the molecule you have drawn; be sure to select GAFF as the force field. Export the resulting configuration as pdb.
3) Using AutoDockTools (adt) from the mgltools package ( convert your pdb file to pdbqt.

There are one or two moments in which you have to be careful when following the procedure outlined above. Mostly, be sure to minimize the molecule with its correct protonation state, and to merge the
non-polar hydrogens when converting to pdbqt.

My second comment is: why do you want to use Autodock4? I suggest you try Autodock Vina ( It's the spiritual successor to Autodock4, and it has several advantages, namely
that it's much faster, much easier to use, and more precise. In addition, if you are an expert user, you can easily tweak with the scoring function, using the options it has, or modifying the source
code, if you prefer. Also, it does not need the fairly cumbersome preparations that Autodock4 needs, such as preparing a grid, the grid files, etc. etc.

I hope this helps. If you have further questions, feel free to ask.



Dr. Charo I. del Genio
Senior Lecturer in Statistical Physics
Applied Mathematics Research Centre (AMRC)
Design Hub
Coventry University Technology Park
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Received on Fri Sep 04 2020 - 02:00:02 PDT
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