AMBER Archive (2009)
Subject: Re: [AMBER] SCC-DFTB MD for mercury ions in proteins
From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Thu Aug 27 2009 - 11:51:21 CDT
The parameters are not coming from amber itself, but rather from DFTB.
Please go to dftb.org 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 Arciauskaite. wrote:
> 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
> AMBER mailing list
Dr. Adrian E. Roitberg
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 adrian_at_qtp.ufl.edu
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