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I am trying to dock a ligand that features a boron (B) atom. AutoDock Vina throws an error with the following message:

ATOM syntax incorrect: "B" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.

I assumed that the error meant that I had to add boron to my Lib\site-packages\AutoDockTools\AD4_parameters.dat file. I found the following parameters for boron in a discussion on the topic:

atom_par B      4.08  0.180  12.052   -0.00110  0.0  0.0  0  -1  -1  4  # Non H-bonding

Together with AD4_parameters.dat, I also added that line to AD4.1_bound.dat, which is in the same directory as AD4_parameters.dat, and to ..\AMDock\programs\AD4Zn.dat file.

But I am still getting the same ATOM syntax incorrect error. Most of the links returned by a web search are from a Scripps Research web site that is no longer available.

Any help would be greatly appreciated.

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2 Answers 2

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As Vina (and other docking software) uses Molecular Mechanics (force-fields) to optimize/score the ligand/protein, in order to use not predefined atoms, you need to generate, by yourself, the force-fields atom's parameters.

You can do that as following:

  • Determine the type of force-fields (equations) used by the Vina.
  • Use a Quantum Mechanical based method (semiemprirical, density functional theory of ab initio) to simulate the interaction of your atom with all other atoms present in the ligand and protein.
  • Fit the force-field potential energy equations to calculations done with Quamtum Mechanics.
  • Add the corresponding parameters to the Vina configuration files.
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  • $\begingroup$ I had hoped that there would be a quicker way. Thanks for your response. This will have to be a longer term approach, but perhaps I should get started on it. $\endgroup$
    – Shredderroy
    Nov 1, 2021 at 16:51
  • $\begingroup$ You always can move to semiempriric or Quantum Mechanic/Molecular Mechanic approaches. $\endgroup$
    – Camps ♦
    Nov 2, 2021 at 14:08
  • $\begingroup$ Thanks again for your suggestion. But isn't molecular dynamics a quantum and molecular mechanical approach? My colleague and I have just found out that gromacs does not work with boron atoms either. If you had something else in mind, any web link would be greatly appreciated, since I am not a biologist or a chemist. $\endgroup$
    – Shredderroy
    Nov 2, 2021 at 15:54
  • $\begingroup$ Molecular dynamics isn't a quantum mechanical method. It is a molecular mechanic one, that's why you need the atom parameters for the force field. $\endgroup$
    – Camps ♦
    Nov 3, 2021 at 12:56
  • $\begingroup$ Take a look here $\endgroup$
    – Camps ♦
    Nov 3, 2021 at 13:12
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If you know the parameters for your new atom_type you can edit the

src/lib/atom_constants.h

file in the source code of vina to add those parameters (name, radius, depth, solvation parameter, volume, covalent radius) and then recompile the package.

If you don't know these parameters for your new atom_type then you follow the method described in the above answer to determine them.

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  • $\begingroup$ +1 and welcome to our new community! Thank you so much for contributing your answer and we hope to see much more fo you in the future !!! Wow you have been on Stack Overflow for a long time! $\endgroup$
    – Nike Dattani
    Mar 14 at 16:30
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    $\begingroup$ Thank you @NikeDattani $\endgroup$
    – UCU110
    Mar 14 at 19:46

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