[gmx-users] ATP+Mg

Алексей Раевский rayevsky85 at gmail.com
Mon Oct 24 10:00:20 CEST 2011

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
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
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*
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111024/9b005c33/attachment.html>

More information about the gromacs.org_gmx-users mailing list