AMBER Archive (2008)

Subject: Re: AMBER: QM/MM simulation

From: Gustavo Seabra (
Date: Sat Nov 22 2008 - 13:19:22 CST

On Sat, Nov 22, 2008 at 10:11 AM, Syed Tarique Moin wrote:

> But do you think about SCF-DFTB support for Iron as mentioned in manual as implemented in amber10.

As Ross mentions, the trans3d parameter set ( contains
Fe, and should work fine in Amber/DFTB. As long as the parameters you
developed are for DFTB and use the correct format for the
Slater-Koster files, I see no reason why they wouldn't work with Amber
as well.

However, note that by "work" I only mean from the program point of
view. We do not test all the parameters. You should make sure they are
appropriate for your system before trying any long calculations. As
stated in the website:

"These sets were created for a special purpose, usually tuned to
reproduce specific properties of selected systems, mostly containing
only a few different type of elements. Their performance for those
systems and properties might be better as of the generic purpose sets
(very often the general purpose sets do not even include those
interactions). They may, however, eventually yield poor results for
other systems and they usually lack an overall test over a broad range
of systems. Please make sure, that you are evaluating those sets
before using them for something different from the systems and
properties they were created for."

Good luck,
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