I am using autodock tool to dock a ligand to a receptor which has Fe ion, but when I run the program I have got a message telling me that Fe ion has zero charge which may affect the docking process. Can you please tell me how can I add charge +3 to Fe ion?
thanks
Thanks Vikash
Is that right if I write +2 or +3 in front of Fe in the pdbqt file? when I opened the pdbqt file generated by the autodock it was 0.000 Fe so I have changed it to +2.000Fe, so do you think that is OK?
In autodoc a metal ion will crash your program.
before starting the scan remove all metal ions/water molecules form the available crystal structure (using chem draw / chimera or any other chem edit software it can be done) and save only the macromolecule and ligand in pdb / mol2 format.
Then before running the grid program add gasteiger charges / coleman charges as per requirement to satisfy the charges on the macromolecule. It will treat the whole system as neutral one.
As autodoc program is written based on gas phase interactions, Fe will not allow to run the program and will give the error massage.
Yup you have done correctly. If Fe is important for the ligand binding then you cannot ignore it. Just gather information about receptor and then assign either +2 or +3 charge.
I don't have much experience with Autodock or Autodock Vina, but I'm pretty sure that the charge of atoms in pdbqt format is never in integer form, always in decimal fraction. I think assigning the charge manually should be done with extra caution.
Hope this help:
http://autodock.scripps.edu/faqs-help/faq/metal-charges
http://autodock.1369657.n2.nabble.com/ADL-calcium-atoms-td2424190.html
Radif
Adding to the above, please refer to this thread:
https://www.researchgate.net/post/How_can_we_change_the_partial_charge_of_a_pdbqt_file_in_autodock
Please let me know if the following is a valid option.
I know from literature that the total charge on the co-factor of my protein is zero. I thus summed the charges for all atoms in the co-factor and it was -1.996, thus I assigned 1.996 charge to the metal center.
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