AMBER Archive (2007)

Subject: Re: AMBER: ptraj: RMS per residues and per time

From: Jianyin Shao (jyshao2004_at_gmail.com)
Date: Fri Jul 06 2007 - 02:54:06 CDT

I guess there is no one simple command for your request. However, it is
possible to achieve what you want by outputting rms value for each residue.
The following code may be helpful to you.

trajin mdcrd
rms first mass *
rms first out rms.1 mass :1 nofit
rms first out rms.2 mass :2 nofit
rms first out rms.3 mass :3 nofit
go

After running ptraj, use "paste" to get the file you want.
paste rms.1 rms.2 rms.3 > rms.tmp
awk '{print $1, $2, $4, $6;}' rms.tmp > rms.all

If you have too many residues, you may want to write a script to get things
done.

Best,

Jianyin

On 7/3/07, Sascha Rehm <SaschaRehm_at_gmx.de> wrote:
>
> Hi all,
>
> is there a ptraj-action (in Amber9) for calculating the RMS for each
> residue and for each timestep? So that I get as result a file with say a
> line for each timestep and a column for each residue which I then can
> plot as a 3D-picture (x=time, y=residue, z=RMS).
> I only know how to plot the RMS for the whole protein vs. the time but
> that's not helpful since I want to see flexible residues through the time.
>
> Thanks for the help,
> regards,
>
> Sacha
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