AMBER Archive (2008)

Subject: RE: AMBER: about RMSD per residue

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Jul 16 2008 - 11:40:42 CDT

Hi,

 

I didn't have time to read the paper hence I just assumed what you wanted was RMSD vs time for each residue. I have no idea what is meant here by "rmsd vs residue number". RMSD for an MD simulation is a function of time and yet your statement has no time variable in it. You probably need to read the paper carefully and see exactly what they mean - perhaps even contact the authors to find out what they did.

 

To get a single number of RMSD vs residue then the options I assume would be:

 

MAX(RMSD per residue vs time)

MEAN(RMSD per residue vs time)

MIN(RMSD per residue vs time) - This would only be meaningful if applying to some reference structure

FINAL(RMSD per residue vs time)

 

All of these you could ultimately get from the data that would be produced from the ptraj script I suggested. It is then a simple matter to reorganize this data to say give you say MAX(RMSD per residue vs time) vs residue number. E.g. just cat the files together before importing them into whatever graphing package you want to use. Or instruct that package to load all the files for you.

 

This is just basic statistical manipulation of data.

 

You will need to think more carefully about what data it is you actually want.

 

All the best

Ross

 

From: luzhenw1_at_msu.edu [mailto:luzhenw1_at_msu.edu]
Sent: Wednesday, July 16, 2008 8:39 AM
To: Ross Walker
Subject: Re: AMBER: about RMSD per residue

 

Hi, Ross:

     i didn't get your idea. RMS can only give you rmsd vs time data. In your ptraj script, the output files (res_00#.dat) give you rmsd(per residue) vs time. In the paper I mentioned, it is actually rmsd vs residue number. Thanks.

 

 

ross_at_rosswalker.co.uk : "Ross Walker" Writes;

You could also just write a quick shell script to generate you a suitable ptraj input script that does the fit you want for each residue. I.e. for a 7 residue system to do a mass weighted RMS fit for all atoms in each residue in turn this might look like:

trajin foo1.mdcrd.gz
trajin foo2.mdcrd.gz
trajin foo3.mdcrd.gz
reference foo_start.inpcrd
image center origin
rms reference mass out res_001.dat :1 name res_001 nofit
rms reference mass out res_002.dat :2 name res_002 nofit
rms reference mass out res_003.dat :3 name res_003 nofit
rms reference mass out res_004.dat :4 name res_004 nofit
rms reference mass out res_005.dat :5 name res_005 nofit
rms reference mass out res_006.dat :6 name res_006 nofit
rms reference mass out res_007.dat :7 name res_007 nofit

I believe this will give something similar to what you were referring to. You can obviously modify the mask to do backbone atoms, a regular rms fit etc.

Good luck,
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Wei Huang
> Sent: Wednesday, July 16, 2008 7:20 AM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: about RMSD per residue
>
> Hi,
>
> As I understood, RMSD per residue should equal to the RMSF of each
> residue. In the paper you mentioned, maybe they used different reference
> structures. For RMSD per residue, maybe the starting structure, so the
> values are larger; for RMSF, maybe the average strucutre.
>
> In ptraj, you can use the 'atomicfluct' to calculate. And set
> different
> reference structures in 'rms' step.
>
> Best,
> Wei
> On Wed, 2008-07-16 at 09:48 -0400, luzhenw1_at_msu.edu wrote:
> > Hi,
> >
> > Thanks for several response. However, I guess I didn't make it
> > clear what RMSD per residue means. There are several papers using RMSD
> > per residue. I am quite sure it is not RMSF and I don't know how to
> > use PTRAJ to calculate. IF you have access to biophysical chemistry,
> > please check this paper:
> >
> > Biophysical Chemistry 130 (2007) 65?75
> > Figure 1C
> >
> >
> > any suggestion about how to calculate it is welcome. Thanks in
> > advance.
> >
> >
> >
> >
> >
>
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