Hi.. I am trying to run a refinement script of an RNA molecule in a periodic box (explicit water). I firstly tried to produce a script that will generate water molecules, which I have done. I then made a script that allowed me to place the RNA molecule inside the water box, to produce an overlay.
My problem is that when I run a refinement script on the overlay, the water molecules do not stay inside the box and disperse away from the RNA. I think I need a periodic boundary script, that will keep the water molecules within the box. I want to send you my files so you can look at them if possible. Thanks Usman
