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

Vaida,
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.

Adrian

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
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
                            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 adrian_at_qtp.ufl.edu

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber