[gmx-users] Genion and number of Ions
marc.saric at mpi-dortmund.mpg.de
Wed Sep 25 15:01:39 CEST 2002
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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