RE: AMBER: problem with calculating RMSD

From: Ross Walker <>
Date: Wed, 18 Apr 2007 09:03:37 -0700

Dear Tri,
The following will do what you want in Carnal:
  PARM p1 1LDY_analogy.prmtop;
  STATIC t1 1LDY_analogy.prmcrd;
  STREAM s1 ../1LDY_prod_300K_10ps.mdcrd.bz2;
  TABLE tab1;
  GROUP solute (RES 1-756);
  RMS fit1 FIT solute s1 t1;
  TABLE tab1 fit1%residues;
Carnal is no longer supported however so unless you have it lying around you
will have to use ptraj. You can almost certainly do the same thing in ptraj
I just have never attempted it. Take a look at the ptraj section of the
manual it should be fairly easy to work out how to do it. Some example
scripts for using ptraj are also included on the amber tutorials
Good luck...
|\oss Walker

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From: [] On Behalf Of
tri nam Vo
Sent: Wednesday, April 18, 2007 01:23
Subject: Re: AMBER: problem with calculating RMSD

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


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
Thank for your helping.

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Received on Sun Apr 22 2007 - 06:07:14 PDT
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