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
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
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.