Re: AMBER: how to calculate the RMSD and B-factor for all atoms of residue

From: Chng Choon-Peng <>
Date: Mon, 6 Mar 2006 17:51:13 +0900

Dear Haixiao,

      Here's what I used, which might serve as a reference for your
own script:
----------- B-factors.ptraj -------------
trajin traj.mdcrd
center origin
atomicfluct out bfac_all-atom.dat :Res1-ResN byatom bfactor
Replace Res1-ResN" with the residue range for the loop.
The keyword here is "byatom".

-------------- RMSD.ptraj --------------
reference Ref..rst
trajin traj.mdcrd
center :Res1-ResN
rms reference out rms.dat :Res1-ResN
I usually have '.CA' behind "Res1-ResN" above, but w/o which should
do for all atoms in the selected residues.
You might wish to center on all residues but only calculate RMSD for
the loop.
All frames in traj.mdcrd will be fitted to that in Ref.rst, to remove
whole molecule
rotations and translations.
Add as many rows of 'trajin' as necessary.

See the PTRAJ webpage for more information:

Hope the above helps.

Choon-Peng Chng

On 2006/03/06, at 17:13, haixiao jin wrote:

> dear Amber users,
> at the most time, we just need to obtain the RMSD and B-factor
> of CA atom or backbone atoms.
> however, to get the conformation change of a special loop in
> MD simulation, the RMSD and B-factor of all atoms in this loop is
> useful. but i do not know how to make the input file for ptraj
> analysis.
> is there anyone who made the input file for analysis the RMSD
> and B-factor for all atoms? i need you help, thank you!

Choon-Peng CHNG
Doctoral Student (Yr 1)
Dept of Computational Biology, Grad Sch of Frontier Science
The University of Tokyo
Affiliated with
Lab. of Molecular Design (Prof KITAO Akio)
Room 107, Institute of Molecular and Cellular Biosciences
1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
Tel: +81 03-5841-1472

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Received on Sun Mar 12 2006 - 06:10:07 PST
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