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 <gustavo.seabra.gmail.com> 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).
Gustavo.
tri nam Vo wrote: Dear everyone,
I've done after the tutorial of amber8 at page
http://amber.scripps.edu/tutorial/integrase/loop11.htm.
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 "ptraj.in" and then run ptraj as follows:
$ ptraj wt1mg.parm7 ptraj.in
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
