Dear List,
Following my problem using ZAFF parameters, I was wondering how I can source the information in ZAFF.xml and ZAFF_param.xml files into Amber.
Cheers,
Siavoush
________________________________
From: Siavoush Dastmalchi [mailto:Dastmalchi.s.tbzmed.ac.ir]
Sent: Thu 7/19/2012 10:03 Þ.Ù
To: AMBER Mailing List
Subject: [AMBER] ZAFF parameters
Dear List,
I am working on a zinc finger protein with two zincs, one ligated by CCCH and the other with CCCO motifs. I was wondering how I can get the amber FF parameters for these zinc containing motifs. I can see that there are ZAFF.xml and ZAFF_param.xml files in amber11/dat/mtkpp/ZAFF directory of my Amber installation and I guess they are based on the paper by MB Peters in J Chem Theory Comput. 2010 September 14; 6(9): 2935–2947.
I will appreciate it if you could kindly let me know if the amber FF parameters for these zinc containing motifs are available for amber users and how I can use that. I am assuming that I need to create pdb coordinate files for the CCCH and CCCO motifs based on solved high resolution structures and also prepare lib and frcmod files for them. Do the coordinate files need to have just ligating residues and zinc atom?
What I have been using so far is based on the message by Ross in
http://archive.ambermd.org/200412/0087.html. I think this method assumes just non-bounded interactions between zinc and atoms in proximity (in the range of cutoff). But the Peters paper takes into account the bonded form as well. Any help will be appreciated.
Cheers,
Siavoush
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Received on Sun Jul 29 2012 - 05:30:02 PDT
