Re: AMBER: problem with calculating RMSD

From: tri nam Vo <>
Date: Wed, 18 Apr 2007 01:22:45 -0700 (PDT)

Dear, Gustavo
 Thank for your helping. I've solved that problem.
 But, I'm trying to study the stability of protein. So, could you tell me how to compare the structures before and after MD by residures? I'd like to know which residure have change in position. Thanks a lot.

Gustavo Seabra <> wrote: The tutorial uses ntwx=5000. If you just changed nstlim to 5000, and did not touch ntwx, you only get one structure in the trajectory file (if any at all).
 tri nam Vo wrote: 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 Sun Apr 22 2007 - 06:07:06 PDT
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