ADL: hemin iron charge

Nisreen Shumayrikh nshumayr at sfu.ca
Tue Mar 4 15:45:54 PST 2014


Hi all!

I am doing some docking with hemin to DNA G-quadruplex structure and I have several questions:

1- in autodock tool, iron charge is assigned to be zero. and when I compute Gasteiger charge ,which assume is for the whole molecule, it gives me -2. I am confused because I understand that the net charge for ferric iron with the four pyrrole rings has to be +1. I changed the iron charge manually in the PDBQT file to +3 and the results were different with regard the energy using vina.

my questions are : 
1-from what I understand about vina, it ignores the charges in the input files, is that correct? how does vina deal with electrostatic interactions?

2- I changed the charge manually by reading the PDBQT file as txt and put +3 instead of the last 0 in the Fe HETAM line, still don't know if this is the right way because when I reopened my file after i did the change, the iron is still zero charged!! could you please guide me how to change charges. 

3- I want to do docking also with autodock 4 version for comparison purpose, however, I got error message saying that K is not defined as an atom. my receptor (DNA) has 2 K atoms, and I need to add its parameters. I did search but I could not find the values, so please if you happen to have them, share with me if possible. would you please help me step by step how to add theses parameters and what to do next to make sure it is added.

Thank you very much!  

Nisreen, 
    


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