AMBER Archive (2006)

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

From: haixiao jin (jinhx952_at_gmail.com)
Date: Tue Mar 07 2006 - 02:10:02 CST

thank you, Choon-Peng!
i want to confirm that, to calculate the B-factor, is it not necessary to
give a reference file and image origin center familar?

On 3/6/06, Chng Choon-Peng <choonpeng_at_cb.k.u-tokyo.ac.jp> wrote:
>
> 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
> image
> 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:
> http://www.chpc.utah.edu/~cheatham/ptraj.html
>
> Hope the above helps.
>
> regards,
> 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
> http://www.iam.u-tokyo.ac.jp/MolDes/indexE.html
> ---------------------------------
>
>
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