[gmx-users] protein molecule fragmenting after addition of counter ions

[jayant james]

Hi all!
I am attempting to counter a charge of -13 in a simulation, where the
protein is solvated in water.  I use the genion option and choose to replace
13 solvent (water) atoms. Upon visualizing the genion output structure, I
find that some atoms from three of the eight cys ( a Hydrogen and two
sulphur atoms ) have be yanked out of the protein! I wonder why this is
happening!!
Is there a way to rectify this?
Thanks
Jayant James

-- 
Jayasundar Jayant James

www.chick.com/reading/tracts/0096/0096_01.asp)
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