Re: AMBER: problem with calculating RMSD

From: Gustavo Seabra <>
Date: Wed, 18 Apr 2007 10:50:21 -0400


I must admit, this is something I haven't done yet, so I can't answer
your question. Here is what I can suggest:

1. Start a new thread on the reflector. Some people might not read all
messages down in a thread, especially if they think that this problem
has been solved. Hopefully, someone with more experience in this field
will step in.

2. Look at your system in VMD. Does it give yopu any hint on what is

3. Look in the manual for the rms command in ptraj. (That's what I would
try first, actually.) If you have any hint of what is moving, you can
use ptraj to calculate the rms for this part with respect to the initial
or a reference structure. (The tutorial example uses the first structure
as reference.)

I hope you'll find the answer to your problem.


tri nam Vo wrote:
> 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).
> Gustavo.
> 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.
>> ------------------------------------------------------------------------
>> Ahhh...imagining that irresistible "new car" smell?
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>> <*;_ylc=X3oDMTE1YW1jcXJ2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDbmV3LWNhcnM->
> ------------------------------------------------------------------------
> Ahhh...imagining that irresistible "new car" smell?
> Check out new cars at Yahoo! Autos.
> <*;_ylc=X3oDMTE1YW1jcXJ2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDbmV3LWNhcnM->

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Received on Sun Apr 22 2007 - 06:07:11 PDT
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