[gmx-users] Add ions on protein

[Mark Abraham]

> Hellow:
>     I have a protein which have 4 calcium ions binding sites,Now I have
> the free
> calcium ions protein, I want to add calcium ions on the binding sites,but
> I know
> the free ions protein conformation is very different to ions loaded
> protein. So I
> want to know whether there is some way to let complex of protein and ions
> to a
> native ca2+ loaded conformation.

You need to choose a force field that you think has some prospects of
modelling the ion-loading sites. Then you need to build a reasonable
starting structure using your chemical knowledge and your favourite
molecule builder - or even hacking them into a structure file by hand.
Then feed that to pdb2gmx and tweak things to get the ions recognised as
part of the molecule and the interactions all what you want. Then you need
to hope that you can relax from the unloaded structure to the loaded
structure in an MD-accesible time frame - or to hack the structure
yourself to achieve that.

These are not simple operations, and I would not recommend this task as a
first exercise in non-trivial MD and/or tweaking protein topologies.
Beware!

Mark