AMBER Archive (2006)

Subject: AMBER: Zn metal library

From: Fenghui Fan (
Date: Sun Nov 05 2006 - 21:51:19 CST

Dear all,

Before we have a tutorial:

Simulating a Solvated Protein that Contains
Non-Standard Residues.

Now this tutorial has been deleted. Does this means
that this method is not so valuble?

I have a protein contains four Zn, each Zn is
cordinated by 4 Cys. Can we say that if we use the
protocol in "Simulating a Solvated Protein that
Contains Non-Standard Residues", only one Zn library
file from one specific Cys can be used for all of the
4 Cys for the MD file construction?

If you do not recommend the simple method, will you
please introduce the basic steps to get the files of
Zin by R.E.D or some other programs to get the small
molecule files?

Best regards.

Fenghui Fan

Everyone is raving about the all-new Yahoo! Mail

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to