AMBER Archive (2003)

Subject: Re: AMBER: MD simulation with ATP and MG

From: Heather A.Carlson (carlsonh_at_umich.edu)
Date: Mon Aug 11 2003 - 07:11:27 CDT

Hi Thomas,

> - Should the posted ATP parameters from Dr. Carlson perform
> well in a MgATP complex?

At the end of our ATP parameter paper (Meagher, Redman, Carlson.
J Comput Chem 2003,24,1016-1025), we show applications to protein
systems all of which include Mg+2 ions. The parameters perform
just fine, comperable to CHARMM.

> - Are the Mg parameters from the parm99 file suitable for
> use with the TIP3P water model?

Should be no problem.

> - Will the complex geometries of Mg and its ligands be
> reasonable, although no Mg-ligand "bond" is defined in the
> parameters?

Yes, in our experience the geometries are OK. Mg is not bound
to ATP, it is just a tight electrostatic attraction. A bond
term is not appropriate.

> - Are there any general caveats for simulations with
> divalent cations?

Your Mg+2 ions are within a protein, right? If so, they are a
structural part of the system. If you have them floating out in
solution, you will have more difficulties with adequate sampling,
but maybe the RNA/DNA modelers will have better insights into
those limitations.

Heather Carlson
 _________________________________________________________________________
       "Black holes are where God divided by zero" Steven Wright

   Heather A. Carlson, Ph.D.
   John Gideon Searle Assistant Professor of Medicinal Chemistry
   Assistant Professor of Chemistry
   Affiliated Faculty, Biophysics Research Division
   Affiliated Faculty, Bioinformatics Program

   http://www.umich.edu/~pharmacy/MedChem/faculty/carlson/

   University of Michigan Phone: (734) 615-6841
   College of Pharmacy (2555 CCL) FAX: (734) 763-2022
   428 Church Street E-mail: carlsonh_at_umich.edu
   Ann Arbor, MI 48109-1065
 _________________________________________________________________________

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