Hi all. I need your advices about my task which is closely associated with ATP toplogy in the binding site. As I understood from one of the letters ( http://archive.ambermd.org/201106/0522.html) I can use antechamber or derive charges from the site linked in the letter. But the ATP's phosphate tail is very flexible and very negatevly charged thus I need too coordinate it with Mg ion to prevent an increased flexibility and motion. Here are some of my questions: 1. What parts of initial structure I have to prepare and process with antechamber - separate adenylate and metal or both of them together like a compound? 2. After getting separate topologys / complex topology - is it necessary to constrain the distances between PO2 groups and metal to be sure this tail won't move anyway during MD or this coordination bond is strong enough?
Thank you -- **** * Nemo me impune lacessit*
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