How should I rename the ‘Zn’ as ‘M’ and provide energy coefficients for Zn in Autodock Tools? I have just started with autodock tools. My protein has Zn ion in it. In the tutorial, it says something about Grid macromolecules.
"ADT also determines the types of atoms in the
macromolecule. AutoDock can accommodate up to 7 atom
types in the macromolecule. It uses a standard set with two
customizable types, ‘X’ and ‘M’. If your macromolecule has a
non-standard atom type, ADT will prompt you to set up a
customizable type X or M for it by entering energy parameters.
For example, Zn is not in the standard set. If your
macromolecule has Zn, for AutoDock you have to rename the
‘Zn’ as ‘M’ and provide energy coefficients for Zn. ‘X’ can
be used as a second customizable type. It is not possible to
have more than 7 types in the macromolecule."
I do not know how to rename and give charge to Zn. Every time I try to save the file as .pdbqt, it gives 0.000 to Zn. [WARNING: These atoms have zero charge: Zn].
I tried using a PDB file editor, but I always do something wrong.
If someone could help in this aspect.
Thank you very much in advance.
Without binding agent we should not dock with protein and metal.so you should conjugate any polymer substance in the outer surface of the metal particle..that will be fine to docking
I edited the pdb file and manually inserted the charge. I came across parameters such as atom radii, and well depth.... do these factors play important role in docking. My metal atom of interest lies in the active site of the receptor
I think the problem is that you're editing the PDB file but not the forcefield parameter file. Whatever 'type' you choose for Zn, there needs to be an appropriate entry in the parameter file. There's a Zn-containing parameter entry in the example "Default Atomic Parameter File AD4.1_bound.dat."
Anyway, I don't think docking (like with AutoDock) is the right idea. An ion is pretty much featureless, and could be docked in many possible locations. I think doing Brownian dynamics with a continuum electrostatic simulation (like BrownDye, linked below) will be better.
At any rate, yes, you need to have the radius and charge correct.
http://browndye.ucsd.edu/browndye/
Those related threads with answers by myself may help, too:
https://www.researchgate.net/post/How_can_we_change_the_partial_charge_of_a_pdbqt_file_in_autodock
https://www.researchgate.net/post/How_can_I_deal_with_metals_in_protein_using_autodock
Few tricks be needed to carryout successfully completion.
1) Update the AD4_parameter.dat according to your necessary metal
2) Update the AD4.1_bound.dat also according to your necessary metal
3) then copy that two files into your installation folder
4) then during grid generation and docking dpf file generation steps, there at set map types option you should mention the required metal atom types and also there is a option named as other option; there u should mention the newly generated parameter file
5) finally the newly generated 2 files should be kept on your docking directory
Finally docking should successfully run.
Hello
I want to enter the copper ion into the parameter file. I edited AD4_parameters.dat and AD4.1_bound.dat files for copper ions and copied them to the installation file. In the docking steps, I entered the AD4_parameters.dat in other options, but it gives the following error:
FATAL ERROR: autogrid4: ERROR: the unbound model cannot be specified in the parameter library file. Use the DPF parameter 'unbound_model' instead.
What should I do?
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