AMBER Archive (2003)

Subject: AMBER: MD simulation with ATP and MG

From: Thomas Steinbrecher (thomas.steinbrecher_at_physchem.uni-freiburg.de)
Date: Mon Aug 11 2003 - 04:45:08 CDT

Dear AMBER users,

I try to do a molecular dynamics run of a protein
containing bound MgATP with amber7.
 
I plan to use the ATP parameters of Dr. Carlson from the
AMBER homepage and I have seen that parameters for the Mg2+
ion are included in the parm99.dat file.

I am rather new to the field of biochemical simulations, so
I have several questions concerning this setup. I searched
the archives and I have found several posts concerning Mg2+
in the archives, but those were mainly questions and no
answers.

It would be very helpful to me if somebody could comment on
the following points:

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

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

- I could not find Mg in ions.lib and ions.cmd, do I have
to add it there? If not how do I tell leap the charge of my
Mg ion?

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

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

Sorry for the long post, and many thanks in advance for any
answers or hints,

kind regards,

Thomas Steinbrecher

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