Re: AMBER: problem with calculating RMSD

From: Gustavo Seabra <>
Date: Tue, 17 Apr 2007 08:41:26 -0400

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 Wed Apr 18 2007 - 06:07:29 PDT
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