[gmx-users] Metal Ion Modelling

Abhishek Acharya abhi117acharya at gmail.com
Wed Nov 15 08:39:25 CET 2017


Each of these models have their own merits and demerits.

Setting up bonded models are non-trivial, but as per my readings, it is
been shown to
work for alkaline and alkaline earth metal ions. So you may try this, but
getting the
correct parameters for the metal-ligand bonds is difficult.

On the other hand, non-bonded spherical model may be easier to parameterize
but i have
had mixed results with these.  Standard parameters available in various
force-fields may work,
but in some cases I have seen the ions diffuse out of the active site. In
these cases, it may
be necessary to calculate the partial charges taking the coordinating
active-site residues into
account. This requires static QM calculations.

Finally, Dummy atom model would be simpler to setup and parameters for OPLS
force-field is
available (check work by Arieh Warshel and Kamerlin). It seem promising as
it has been show
to allow correct dynamics of the protein and also supports ligand exchange
processes. But
according to my knowledge, it hasn't been used much for studying protein
dynamics as yet.

You can try both the non-bonded and dummy model and see compare the results.

Abhishek Acharya

On Sat, Nov 11, 2017 at 4:15 PM, Quyen V. Vu <vuqv.phys at gmail.com> wrote:

> Dear GMX community,
> I want to simulate a long simulation of enzyme, ligands and metal cofactor
> (Mg2+), we also have NACL salt in the environment.
> I know that there are three model of metal ion: Bonded, Nonbonded, and
> Cationic Dummy atom.
> So which model for Mg2+ should I use in this case?
> Thank you in advance!
> Quyen
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