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AMBER Archive (2009)Subject: [AMBER] RE: ask for help (zn parameters)
From: Ross Walker (ross_at_rosswalker.co.uk)
Hi Yaxue,
I am copying this message to the AMBER mailing list which is where such questions should be posted. See http://lists.ambermd.org/ for signup details.
To comment on your questions. Firstly please be aware that the parameters for copper in the tutorial you refer to were made up purely for the purposes of the tutorial and as stated in the tutorial are not to be used for actual production simulations. With regards to your questions you could take a look at my Ph.D. thesis:
http://www.rosswalker.co.uk/files/Ross_Walker_Thesis_Final.pdf
This has parameters for zinc bound to cysteine's and histidines adapted from Ryde. This should cover all the parameters you need since it contains a Zn-Cys2,His,CXF system. Which should provide you with dihedrals for CYS-Zn-CYS and CYZ-ZN-HIS which should be all you need. You will need to build yourself a frcmod based on the parameters here and the names of the atom types you use in your system.
All the best
Ross
From: 赵亚雪 [mailto:xue424_at_yahoo.com.cn]
Dear Prof. Ross,
Best regards!
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