[gmx-users] How to set the charge of zn and cys!
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
J.B.S. Haldane, preface to "What is Life?", Lindsay Drummond, 1949
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