AMBER Archive (2008)

Subject: RE: AMBER: about RMSD per residue

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Jul 16 2008 - 09:52:38 CDT

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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