[gmx-users] How to define the protonated state of a protein

Eric Jakobsson jake at ncsa.uiuc.edu
Fri Oct 29 05:48:33 CEST 2004

The protonation state for a residue in a particular protein may be 
different from the residue's protonation state in solution, so to be more 
confident you have it right you need to do a pK calculation, which takes 
into account other charges in the protein and the fact that the bulk of the 
protein has different dielectric properties from electrolyte.


At 01:52 AM 10/29/2004 +0800, you wrote:
>Dear gmx-users£¬
>I am a newbie in protein simulation. So maybe my question is so silly.
>In my protein, there is Asp Glu His Arg and Lys. I what to user pdb2gmx 
>-inter to specify the protonated state of this residue. But I don't have 
>any experience on it. Could anybody give me a help?
>The following is my view, is it right? Please help me to correct it?
>I assume the pH value is equal 7.
>Thank you in advance!
>Sincerely yours
>PeiQuan Chen
>PeiQuan Chen, Ph.D Student, Department of Chemistry, Nankai University
>WeiJin Road 94, TianJin, 300071, P.R.China
>phone:  (86)2223507510(HOME) (86)23505264 Mobile Phone: (+86)13920675030
>pqchen at mail.nankai.edu.cn
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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909
(Currently on leave to the National Institutes of Health in Bethesda, 
Maryland, to be Director of the NIGMS Center for Bioinformatics and 
Computational Biology and Chair of the NIH Biomedical Information Science 
and Technology Initiative Consortium, but maintaining my research lab at 
Illinois by periodic commuting.  My usual schedule is four days a week at 
NIH and three days a week at Illinois.)

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