AMBER Archive (2006)

Subject: Re: AMBER: Zn metal library

From: Carlos Simmerling (
Date: Mon Nov 06 2006 - 06:26:52 CST

Dear Fenghui,
the Amber tutorials are very nice and Ross worked hard to put them
together. However, based on a lot of your email questions you seem
to be using them as a primary reference for how to do proper
simulations, and you supplement that with questions here.
I strongly recommend that you change your thinking about this
and treat published journal articles as the primary source of
information about
how simulations should be done, and this email list and the tutorials
for more technical questions about sander inputs, errors, etc. Most of
the questions that you have been asking are clearly addressed in the
literature and the data there have been peer-reviewed. The whole
reason that we all publish papers is for people like you to read them
and see our methods and our results. You should be going to papers that
do work similar to what you want (like ones that do simulations with zinc)
and see what they used and how good the results are. Asking people
to repeat all of that here is not likely to get you any answers.
Learning to read and use the literature is a very important part of
being a successful scientist, please don't ask here for us to repeat things
that we have already put a lot of effort into describing in our
Instead you should spend your time reading articles and ask the authors
if something isn't clear. Ask on this list if you have a technical problem
with Amber.
good luck with your simulations!

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail:
Stony Brook, NY 11794-5115 Web:

Fenghui Fan wrote:

>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
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