Maybe it would be easier (better) to use the ATP parameters that have bee posted at:
http://www.pharmacy.manchester.ac.uk/bryce/amber#cof
Pete Gannett
________________________________________
From: Алексей Раевский [rayevsky85.gmail.com]
Sent: Monday, October 24, 2011 3:59 AM
To: AMBER Mailing List
Subject: [AMBER] ATP+Mg
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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Received on Mon Oct 24 2011 - 04:30:04 PDT
