ADL: hemin iron charge

Nisreen Shumayrikh nshumayr at sfu.ca
Tue Mar 11 00:36:39 PDT 2014


Thanks for reply! 

I just opened the PDBQT file (after preparation and saving)with Notepad, edited the Fe charge to +3. No problem when I run vina with the edited file, however, when I reopened the edited file using ADT, compute Gastegeir charge, ADT did not recognize the edited charge. Why?

the results I got with the edited file is almost the same with the non edited file, so I am wondering weather vina recognize the edited charge as well?! 

could you please comment on that?? 


Thanks, 

Nisreen  
  

----- Original Message -----
From: "Oleg Trott" <trott at scripps.edu>
To: autodock at scripps.edu
Sent: Tuesday, 4 March, 2014 16:37:07
Subject: Re: ADL: hemin iron charge

On Tue, Mar 4, 2014 at 4:27 PM, Nisreen Shumayrikh <nshumayr at sfu.ca> wrote:
> Thanks for replying!
>
> for question 2: I was able to change the charge in txt file, ADT did not reflect the change! why?

My guess is that your edit violated the syntactic conventions of the
file format. Try feeding the edited file to Vina. If it's bad, Vina
should reject it.

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

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com
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