[gmx-users] Genion and number of Ions

Marc Saric marc.saric at mpi-dortmund.mpg.de
Wed Sep 25 15:01:39 CEST 2002

Hi all,

this might be a beginners question, but I have some problems with genion:

I want to simulate a comparably large (~70 kDa) protein complex (three 
single protein molecules one ligand and some water in a solvent-environment.

I did all steps as described in the tutorial: pdb2gmx, addition of the 
ligand-topology from PRODRG as described in the tutorial from John E. 
Kerrigan, solvation with editconf and genbox, compilation with grompp, 
addition of ions with genion.

1. Question: A friend of mine, who knows a bit more about MD-Simulation 
than I, told me to make a neutral setup i.e. add as many ions as 
necessary to bring the total charge to 0. Is there any other suggestion 
(at the moment I add only a few Na+-Ions, but this doesn't sound  too 
reasonable to me).

2. Question: What to do with fractional charges (i.e. -3.2 ?)

Is there any program or rule of thumb to decide on the amount of ions 

3. Question: Genion asks for a continuos solvent-group of single-atom 
molecules. My solvent seems to be split in halfes, due to the 
incorporation of the crystal-waters and later the addition of the ligand 
and after that addition of the waterbox. Any hint how to overcome this 
(beside processing the crystal-waters separately and adding them 
afterwards by hand, which is quite tedious (renumbering etc.)).

Thanks in advance!

Bye,  Marc Saric

Max-Planck-Institut fuer molekulare Physiologie
Otto-Hahn-Str.11  44227 Dortmund  phone:0231/133-2168

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