AMBER Archive (2007)

Subject: AMBER: calculate RMSD of only chain C

From: 赵亚雪 (xue424_at_yahoo.com.cn)
Date: Fri Mar 02 2007 - 20:21:33 CST

hello,
  I do molecular dynamics simulation with amber9. My system contains three chains - A,B and C. Now I want to calculate the RMSD of only chain C, and set the parameters as follows:
   
  rms reference out md1-13C_rmsd :306-387_at_CA,C,N
   
  But what really does the setting mean: (I suppose three)
  1. Fit the chain C of trajectory to the chain C of reference and calculate the RMSD of only chain C
  2. Fit the chain C of trajectory to the chain C of reference and calculate the RMSD of three chains
  3. Fit the three chains of trajectory to the three chains of reference and calculate the RMSD of only chain C
   
  Which one is right of the three possibility (1. 2. 3.)? What I want to get is the first one. If it does not mean the first, how can I set the parameter to get it?
   
  Thanks very much!
  Yaxue Zhao
  Lab of molecular Modeing and Design
  School of Pharmacy
  East China University of Science and Technology
  Mailbox 268
  130 Mei Long Road
  Shanghai 200237,China
  Tel: +86-21-64251190
  E-mail:xue424_at_yahoo.com.cn

                 
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