[Chimera-users] Regarding getting zwitter-ionic stucture of beta-alanine

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 9 08:29:58 PST 2018


Hi Dilip,
Just get the PubChem beta-alanine (neutral), and then delete hydrogens and add them back in Chimera.  Chimera recognizes the functional groups and makes the zwitterion. For example, commands:

open pubchem:239
delete H
addh

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 8, 2018, at 9:44 PM, Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:
> 
> Ie.,
> The beta-alanine neutral form is in NH2-CH2-CH2-COOH, but i want its zwitterionic form which is NH3+-CH2-CH2-COO-
> Any suggestions..??
> Thank you.
> 
> On Fri, Feb 9, 2018 at 10:37 AM, Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:
> 
> Hello,
> I was able to get the beta-alanine neutral structure in chimera using the PubChem id ie., 239.
> But i want beta-alanine in its zwitterionic form since in water systems it will be in more stable in zwitterionic and i can run the simulation. 
> 
> So, how do i get it in zwitterionic form..??
> Any suggestions are appreciated.




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