AMBER: problem with calculating RMSD

From: tri nam Vo <>
Date: Tue, 17 Apr 2007 00:01:35 -0700 (PDT)

Dear everyone,
  I've done after the tutorial of amber8 at page
  Reimaging trajectory input:
  trajin wt1mg_eq.crd
center :1-154
image center familiar
rms first out wt1mg_eq_rms.out :3-152.CA
trajout wt1mg_eq_nice.crd nobox
  save this input and call it "" and then run ptraj as follows:
  $ ptraj wt1mg.parm7
  I just test so I did just nstlim=5000 (instead of 50000 as in tutorial).
  And I've received out file with just one line: 1.00 0.00000
  Could anyone tell me the reason of it?
  By the way, I want to learn how to compare the structure of my protein by residure before and after MD. (I want to know which residure have change in position).
  Thank for your helping.

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Received on Wed Apr 18 2007 - 06:07:25 PDT
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