AMBER Archive (2009)

Subject: Re: [AMBER] SCC-DFTB MD for mercury ions in proteins

From: Adrian Roitberg (
Date: Thu Aug 27 2009 - 11:51:21 CDT

The parameters are not coming from amber itself, but rather from DFTB.
Please go to and see if they have the parameters. If they do,
Amber can be made to read them, I think without much hassle.

One caveat: Amber's implementation of dftb does not have, so far,
d-orbital support. So, if the dftb parameters themselves are written
with d-orbitals, they will not work.


Vaida Arcišauskaite. wrote:
> Hello,
> I would like to ask if the SCC-DFTB method for hybrid QM/MM
> simulations within the Amber Molecular Dynamics Package has been
> parametrized for mercury ions (Hg2+) in proteins?
> Thank you very much for your attention and looking forward to hear from you.
> Vaida Arcisauskaite
> PhD student at LIFE faculty
> University of Copenhagen
> Denmark
> _______________________________________________
> AMBER mailing list

                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry

Senior Editor. Journal of Physical Chemistry American Chemical Society

University of Florida PHONE 352 392-6972 P.O. Box 118435 FAX 352 392-8722 Gainesville, FL 32611-8435 Email

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