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

jayant james jayant.james at gmail.com
Thu Jun 5 04:36:39 CEST 2008

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
Is there a way to rectify this?
Jayant James

Jayasundar Jayant James

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