AMBER Archive (2005)

Subject: AMBER: Metals with Amber

From: Anton B. Guliaev (abguliaev_at_lbl.gov)
Date: Fri Oct 28 2005 - 12:09:07 CDT

Dear Amber Users,

We are currently interested in doing some MD simulations to study
interactions between the proteins and different metal ions, such as Zn,
Cd or As (identification of possible binding sites?). I would really
appreciate any feedback regarding the current standing of computational
approaches for the modeling of protein interactions with the different
metals ions. Basically, we are wondering how well the current Amber
force field reproduces such interactions? And would the differences
between two positively charged cations: like Zn2+ or Cd2+ be well
represented? Or will they be treated as similar entities by Amber?

I know that Zn2+ parameters are available for the Amber... does anybody
developed parameters for Cadmium (Cd2+) or Arsenic (As)....

Any inputs are greatly appreciated.

regards,

Anton (LBNL, Berkeley) 

--
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        * Anton B. Guliaev, Ph.D  *
        * Life Sciences Division  *
      _ * LBNL, Berkeley CA 94720 * _
     / )* abguliaev_at_lbl.gov       *( \
    / / * F:(510)-486-6488        * \ \
  _( (_ * T: 510-486-5773         *  ) )_
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