From: Ana Celia Araujo Vila Verde (avilaverde_at_engr.psu.edu)
Date: Fri Jun 08 2007 - 09:58:58 CDT
1) I found articles in the literature where people investigated adsorption of proteins on gold using parameters obtained in two articles. Unfortunately, I believe that both those sets of parameters are entirely incorrect for this application... In any case you should make your own judgment about it, so here they are:
Rappe, A.K., et al., Uff, a Full Periodic-Table Force-Field for Molecular Mechanics and Molecular-Dynamics Simulations. Journal of the American Chemical Society, 1992. 114(25): p. 10024-10035. (the parameters reported here are appropriate for gold ions complexed with molecules, not for gold atoms)
Halicioglu, T. and G.M. Pound, Calculation of Potential-Energy Parameters from Crystalline State Properties. Physica Status Solidi a-Applied Research, 1975. 30(2): p. 619-623. (the parameters reported here are appropriate for interactions of gold atoms with other gold atoms (or other metal atoms at best) via metallic bond, but not for adsorption of proteins to gold).
2) Spohr developed a set of parameters for gold but they cannot be used in NAMD. Spohr, E., Ion Adsorption on Metal-Surfaces - the Role of Water-Metal Interactions. Journal of Molecular Liquids, 1995. 64(1-2): p. 91-100.
3) I developed my own set of parameters for gold but I haven't published yet. I can send you a reprint as soon as I do.
I hope this helps...
Ana CÚlia Ara˙jo Vila Verde
Penn State University
Department of Chemical Engineering
University Park, PA 16802
Phone: +(1) (814) 863-2879
Fax: +(1) (814) 865-7846
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of utiramerur_at_ecr6.ohio-state.edu
Sent: Friday, June 08, 2007 9:52 AM
Subject: namd-l: Parameter file for Gold ?
Hello, dose anyone have parameter files for Gold. I am trying to simulated a system with Polymer tethered to Gold surface.
Any help is greately appreciated.
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