[AMBER] RE: ask for help (zn parameters)

From: Ross Walker <ross.rosswalker.co.uk>
Date: Mon, 6 Jul 2009 03:56:50 +0100

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:




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




From: 赵亚雪 [mailto:xue424.yahoo.com.cn]
Sent: Monday, June 29, 2009 12:31 AM
To: ross.rosswalker.co.uk
Subject: ask for help (zn parameters)


Dear Prof. Ross,
  I am Yaxue Zhao, a student of Shanghai Jiaotong university. I use Amber software to
simulate a protein which contains two Zn atom. one Zn atom bond to 4 Cys, and the other
Zn atom bond to 3 Cys and 1 His.
  I have created ZNA.lib and frcmod.zna files as you described in "Amber Mail Reflector"
(attached file1). Also I missing some parameters about Zn atom just like
Annette.(attached file2). Also you suggested Annette to obtain the parameters from "Ryde,
U., Proteins: Structure, Function and Genetics, 21:40-56 (1995)". I have read the paper
(attached file3), but I can not find all the missing parameters in the paper.
  There is a very good and useful example you wrote to us
(http://ambermd.org/tutorials/advanced/tutorial1_orig/). And you offered a very detail
parameters about Cu atom in that example (attached file4).
  And here I want to know if you have the Zn parameters just like Cu(plc.frcmod, attached
file4). The Zn parameters are very important for me. And I expect your help. Thank you
very much!

Best regards!



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Received on Mon Jul 06 2009 - 17:35:48 PDT
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