AMBER: Force fields for iron

From: MARY O'CONNOR <MOCONNOR.westliberty.edu>
Date: Mon, 05 Feb 2007 16:19:52 GMT

Hello, all:

     My question, in essence, is a request for a tutorial or step by step "recipe" for taking a molecule optimized in Gaussian , taking the data from the optimization run, and making new force field parameters for, in my case, heme iron. O have bond lengths from the J McNamara paper in J Comp Chem 27:1307, 2006. But, what other information do I need? How do I calculate cross-terms? At this point, only the structures have been established.

  There seem to be a great many messages on the board about how to do this. There are no (or I have not found) literature that thoroughly explains the process.

So, the simplest way I  can put my question is : I have bond distance data for a training set for heme iron of about 50 molecules. Where do I go from there?

Thanks,

Mary

M.V. O'Connor, Ph.D.
West Liberty State College
139 Campus Service Center
West Liberty, WV 26074
Office : (304) 336 - 8394
e-mail:moconnor.westliberty.edu

       
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Received on Wed Feb 07 2007 - 06:07:21 PST