I´ve tried to docking copper complex to protein with autodock. But, several parameters for this metal ion, founded in the web, do not work. At the finish results the program recognize it as Carbon atom.
I need:
1. vdW well depth (in Kcal/mol)
2. atomic solvation volume (in Angstrom^3)
Thanks
Hi, Find them in the link below
http://mgldev.scripps.edu/pipermail/autodock/2009-March/005439.html
Edit the file "AD4_parameters.dat" to add the parameters. Good luck!
You need to generate a parameter file for Copper. For that you can modify .gpf and .dpf files. An example of modification is as follow: For metal ions, an example entry in the parameter file is: atom_par Zn 1.48 0.550 1.7000 -0.00110 0.0 0.0 0 -1 -1 4 The first four numbers are the ones to change: Rii = sum of vdW radii of two like atoms (in Angstrom) epsii = vdW well depth (in Kcal/mol) vol = atomic solvation volume (in Angstrom^3) (4/3*pi*(Rii/2)**3) solpar = atomic solvation parameter . You can edit those files by Notepad++ or Vim and ...
I am using Autodock 4.2 program. I have a Cu (copper complex) metal ion in my ligand molecule. I entered all the data for Cu in the parameter file and was able to autogrid. However, even though I define the same parameter file in the dpf file, I get the error 'I can't find or open AD4_parameters' while Autodock. What could be the reason?
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