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.umich.edu
Ann Arbor, MI 48109-1065
_________________________________________________________________________
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Received on Mon Aug 11 2003 - 13:53:01 PDT
