[Chimera-users] Charge assignment to a ligand

Prabuddha Bhattacharya b.prabuddha3 at gmail.com
Mon Apr 13 11:51:08 PDT 2020

Dear Sir,

I had a query regarding charge assignment to any ligand in chimera.

While minimizing the energy of a particular ligand (Tools --> Structure
Editing --> Minimize Structure) and also during Dock Prep, I found that for
most of the aliphatic and alicyclic amines, they are getting protonated
with a residual positive charge; while the aromatic amines remain
unprotonated (and hence no residual charge). I understand that this is
because of their differential pKb values (basic strengths).

On the other side, deprotonation never occurs with the carboxylic acid
(-COOH) group.

Does the Chimera (force fields) control this issue of protonation and
deprotonation considering the physiological pH ?

I will be extremely grateful if some one may kindly clarify my doubts.

Thanking you in advance,

With Best Regards,

*Dr. Prabuddha Bhattacharya *
*Dept. Of Chemistry*
*Adamas University*
*Kolkata 700126*
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