ADL: hemin iron charge

Nisreen Shumayrikh nshumayr at sfu.ca
Tue Mar 4 16:27:42 PST 2014


Thanks for replying! 

for question 2: I was able to change the charge in txt file, ADT did not reflect the change! why? 

Regards, 

Nisreen 
----- Original Message -----
From: "Oleg Trott" <trott at scripps.edu>
To: autodock at scripps.edu
Sent: Tuesday, March 4, 2014 4:10:42 PM
Subject: Re: ADL: hemin iron charge

Hi

On Tue, Mar 4, 2014 at 3:45 PM, Nisreen Shumayrikh <nshumayr at sfu.ca> wrote:
> 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?
>

There have been quite a few discussions about this:

https://www.google.com/search?q=autodock+vina+electrostatic+trott+site:mgldev.scripps.edu

> 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.
>

Are you saying you were unable to edit a text file on your computer,
or that some viewer did not reflect your changes?

> 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.
>

This FAQ seems relevant:
http://autodock.scripps.edu/faqs-help/faq/how-do-i-add-new-atom-types-to-autodock-4

HTH

-- 
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com

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