I have a protein-ligand docking project. The ligand contains boron atoms that are not detected by Autodock software. To solve this problem, it is necessary to introduce the boron atom to Autodock, for this case the parameters of the potential shell well and atomic solvation is required.
But I do not find the exact value of these two parameters. Does anyone have these parameters for a boron atom?
Hi,
I once had the same problem and I found this:
http://autodock.1369657.n2.nabble.com/ADL-Parameters-for-docking-with-metal-ions-in-receptor-td2505649.html
I don't think they are validated, but you can try them (I have tried sodium, with apparently no problem). Here is the one for boron:
atom_par B 4.08 0.180 12.052 -0.00110 0.0 0.0 0 -1 -1 0
Hope it helps!
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