[gmx-users] How to set the charge of zn and cys!

Mikko Hellgren Mikko.Hellgren at mbb.ki.se
Thu Dec 15 11:09:54 CET 2005

Hi all, I would like to get some advice of how to set the charge of a 
zinc ion non covalent bonded to cys(1,2,3 or 4 cys) in a small peptide 
23AA. According to some QM calculation (ref U. Ryde) the cys become 
deprotonated and have the S atom have an electro-negative charge of -
0.75 (4cys-zn) and the zn have a positive charge of about 1, giving a 
total negative charge of -2 (4*-0.75+1=-2). I have three different 

1. How to set cys deprotonated in Gromacs? 
2. Is charge -0.75 for S in Cys and +1 for zn OK to start with or 
should i try something else? In that case how to set the charge on the 
CH2 side group.
3. One could expect that the charge distribution change in cys due to 1-
4 cys coordinated to zinc? If this is the case, how to simulate this or 
should this effect be ignored.

Question number one is probably a very general one, and I think it 
should be implemented in pdb2gmx (I am not the person to do it 

Many thanks for all suggestions.

Mikko Hellgren, PhD student at Karolinska Institutet in Sweden
mikko.hellgren at ki.se

One cannot avoid making mistakes if one tries to produce a set of 
words, or of mathematical formulae, to describe nature. Nature is more 
complicated than language or mathematics. Nevertheless, one must do 
one's best to produce a set of symbols which are not to discordant with 
the facts.
J.B.S. Haldane, preface to "What is Life?", Lindsay Drummond, 1949
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