Regarding getting zwitter-ionic stucture of beta-alanine
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. -- With Best Regards, DILIP.H.N Ph.D Student <https://mailtrack.io/> Sent with Mailtrack <https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality>
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. <https://mailtrack.io/> Sent with Mailtrack <https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality> On Fri, Feb 9, 2018 at 10:37 AM, Dilip H N <cy16f01.dilip@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.
-- With Best Regards,
DILIP.H.N Ph.D Student
<https://mailtrack.io/> Sent with Mailtrack <https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality>
-- With Best Regards, DILIP.H.N Ph.D Student
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@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@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.
participants (2)
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Dilip H N -
Elaine Meng