It is currently Sun Jul 22, 2018 12:21 pm

All times are UTC




 Page 1 of 1 [ 4 posts ] 
Author Message
 Post subject: A nitrogen atom being wrongly protonated
PostPosted: Wed Apr 06, 2016 4:47 am 

Joined: Fri Apr 01, 2016 10:58 pm
Posts: 1
Hi all,

After I draw a ligand, no matter which method I use for geometry optimization,
one of the nitrogen atoms in my aromatic ring is protonated incorrectly (picture attached),
making it have 4 bonds which I don't think I want it.

Could anyone please suggest how I could fix this problem?

Thanks,
Jay


Offline
 Profile  
 
 Post subject: Re: A nitrogen atom being wrongly protonated
PostPosted: Wed Apr 06, 2016 7:20 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 204
Hi, try changing pH, it should help.


Offline
 Profile  
 
 Post subject: Re: A nitrogen atom being wrongly protonated
PostPosted: Wed Apr 06, 2016 7:43 pm 

Joined: Mon Apr 04, 2016 1:40 am
Posts: 1
Hi,

Thanks for the response; it does help! But I wonder if I should input the pH under physiological condition or the lowest pH that my compound is not protonated for docking calculation. Btw, my compound has an iso-cytosine ring contained in it.

Thanks in advance.

Jay


Offline
 Profile  
 
 Post subject: Re: A nitrogen atom being wrongly protonated
PostPosted: Sat Apr 09, 2016 9:51 am 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 204
You should try docking with different pHs if protonation is crucial in your system (docking will use the ligand in the form you prepared; protonated at low pH). Since local pH in the protein binding site can be very different from physiological condition, there is no golden rule which is the appropriate choice but you should consider your protein and known ligands.


Offline
 Profile  
 
Display posts from previous:  Sort by  
 Page 1 of 1 [ 4 posts ] 

All times are UTC


You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot post attachments in this forum

Search for:
Jump to:  

cron