[gmx-users] How to add calcium ions at desired position?

[Mark Abraham]

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