Dear rayevsky85,
An answer to the problem you report is the strategy developed by
R.E.D. and/or R.E.D. Server at
http://q4md-forcefieldtools.org/ :
Instead of considering ATP as a whole molecule with multiple negative
charges and with many putative (& non-representative?) conformations a
possible approach consists in splitting the target molecule (ATP) into
elementary building blocks.
Following this building block strategy we have generated many FF
libraries for the most common biochemical cofactors; among them a
consistent approach is applied for AMP, ADP, ATP, AQP, A5P and more
generally for XYP (X = the regular bases; Y integer value > 0) and
even more.
We finally submitted the corresponding data in the reviewing process
of R.E.DD.B. Should be available soon... See the reviewing part of
R.E.DD.B....
regards, Francois
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 26 2011 - 09:00:02 PDT
