Peggy Yao wrote:
Hi all,
I would like to simulate a protein with calcium ions at the calcium
binding sties. I cannot use genion to add calcium ions because genion
put the ions randomly. Is there any conventional way to do this?
If you read the man page for genion, you can get some ions generated at
points where the electrostatic potential would suggest placing them,
which are likely to be your binding sites.
I'd echo the other guys' advice, and suggest that you first get your
setup and equilibration protocol working without worrying about
precisely placing calcium. The same topology will work with Ca+ placed
wherever you like later on.
Also check out
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
Mark
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