AMBER Archive (2007)

Subject: AMBER: How do I make and enter new ff parameters into AMBER

From: MARY O'CONNOR (MOCONNOR_at_westliberty.edu)
Date: Fri Feb 02 2007 - 13:35:20 CST

HellO

     I need to generate and enter into AMBER new Fe parameters for heme iron. I have the paper by J <cNamara et al (J Comp Chem 27:1307 2006) in which he lists bond lengths, etc. for heme iron models. I have never done thus type of work before, and if I don't do it, I will probably lose my funding. So, if anyone could take me step-by=step through generating force field parameters, tell me exactly what kind of data I need, and how to change the parameter code in AMBER, I would be extremely grateful. I have tried to read up on how to do this through papers and web sites, but a.) I am EXTREMELY visually impaired and b.) no one ever tells the whole story.

 

Thank-you very much

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

       
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu