[gmx-users] About ADP

[Eric Jakobsson]

Protonation states are very context-dependent, see Varma and Jakobsson in 
Biophysical Journal just a month or so ago for our group's most recent work 
on that.

At 07:33 PM 3/14/2004 +0800, you wrote:
>Dear gmx-users £¬
>     I want to produce topol file of ADP with dundee server, what kind of 
> protonate state should be choosed? that is, how many protons should be 
> added to the negative "O" in "P-O-"?
>
>            _
>           O
>           |  _
>         O=P-O
>           |
>           O
>           |  _
>         O=P-O
>           |
>           O
>           |
>          ...
>          (1)
>
>
>           OH
>           |  _
>         O=P-O
>           |
>           O
>           |  _
>         O=P-O
>           |
>           O
>           |
>          ...
>          (2)
>
>
>that equals to say, (1) or (2) should be choosed for the dundee server input?
>
>
>Best Regard!
>                                  Zhiguo Liu
>                                  DDDC
>                                  Chinese Academy of Science
>                                  Shanghai,China
>                                  zgliu at iris3.simm.ac.cn
>                                  2004-03-14
>
>
>
>
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---------------------------------
Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Biochemistry
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
405 N. Mathews Avenue
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909

(Currently on leave to NIH to serve as Director of Center for 
Bioinformatics and Computational Biology at the National Institute of 
General Medical Sciences and Chair of the NIH Biomedical Information 
Science and Technology Initiative Consortium.  Usual schedule is four days 
a week at NIH and three days a week at Illlinois.)