Re: How to decide the protonation of some residues??

From: Brian Bennion (
Date: Wed Nov 03 2004 - 10:35:07 CST


This has been discussed before on the list. Do a quick search...

Briefly, unless you have data from NMR titration experiments or good
data from statistical mechanics calculations it is not possible to predict
protonation states better than 50-50.


On Wed, 3 Nov 2004, mashaojie163 wrote:

> Hi:
> I know you should construct the model with correct protonation state if you want to do simulation in some acid solvate. Do you tell me how to decide the protonation of some residue, for example HIS, Asp, Tyr, Arg, Leu, Glu .etc.
> Best regards
> Ma Shaojie

**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **

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