On Tue, Sep 01, 2009, Timothy Robbins (trobbins) wrote:
>
> I want to create a set parameters or a library file that will allow me
> to add Al3+ counterions to a generic DNA oligonucleotide. If at all
> possible I would like to be able to use these Aluminum ions like the
> counterions built into Amber10 already such as Na+ or Mg2+. Anybody have
> any suggestions or know how in this area? Thank you for any help you can
> provide.
Technical answer:
Edit $AMBERHOME/dat/leap/lib/ions94.lib and add your Al3+ residue by analogy.
Edit $AMBERHOME/dat/leap/parm/frcmod.ionsjc_spce (or a similar file) to add
the mass and Lennard Jones parameters.
More "scientific" answer:
The procedure above will allow calculations to be run, but it is unlikely
to give good physical results, compared to "real" aluminum ions. There
is presumably a fair amount of charge transfer between the waters in the
first hydration shell and the metal ion. Even divalent ions are quite
difficult to model just as point charges with Lennard-Jones terms added. So
you will want to think hard (and study the literature) about what properties
of the system you are trying to simulate.
...dac
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Received on Wed Sep 02 2009 - 23:07:29 PDT
