Hello,
I am working on a protein that belongs to NUDIX family hydrolases and therefore requires Mg ion as a cofactor. But the protein that I have downloaded from PDB is an apoprotein. I want to include Mg ion also in my docking and MD simulations. I have schrodinger software. Can anyone suggest me how to proceed with this problem?
I'm not sure about Schrodinger Maestro (if they have special tools for specific ion adding) but as I remember there are some online servers where you can place desired ion in PDB structure:
Moreover, you can just add a string in your PDB file. For example, like in 7cff:
HETATM 1178 MG MG A 202 7.041 42.084 22.273 1.00 27.09 MG
But you have to know where you need your ion.
Or you can try to open your PDB structure via any molecular visualisation software (such as Avogadro or similar) and add ion.
- Badges
- Science method