As to the second question, depends on what you want to know. However, constraining things, I think, should be done with caution.
Pete Gannett
________________________________________
From: Алексей Раевский [rayevsky85.gmail.com]
Sent: Monday, October 24, 2011 8:30 AM
To: AMBER Mailing List
Subject: Re: [AMBER] ATP+Mg
Yes I think so too. Thank you for reply. Can I ask you? Do you have any
suggestions about second problem???
Sorry for such obsession!
24 октября 2011 г. 14:18 пользователь Gannett, Peter
<pgannett.hsc.wvu.edu>написал:
> 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
> --
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Received on Mon Oct 24 2011 - 06:00:05 PDT
