AMBER Archive (2006)

Subject: Re: AMBER: RMS & PCA

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Mon Jul 17 2006 - 13:22:56 CDT

Hi,

> 1. Is it possible to rms fit structures with respect to backbone atoms,
> but get a residue by residue rmsd, like residue 1 compared to residue 1
> of the reference structure?
You can certainly calculate residue RMSD for a single structure or a
trajectory. If you am familiar with VMD, below is a python script that
calculate the average residue RMSD for a trajectory.

import molecule
from AtomSel import AtomSel

molid = molecule.new("trajectory")
molecule.read(molid, "parm7", "CK_TSAC.cym276.top", waitfor=-1)
molecule.read(molid, "crd", "cym.nowat.x", waitfor=-1)

refid = molecule.new("reference")
molecule.read(refid, "parm7", "CK_TSAC.cym276.top", waitfor=-1)
molecule.read(refid, "rst7", "CK_TSAC.cym276.crd", waitfor=-1)

nframe = molecule.numframes(molid)
ref = AtomSel("backbone", refid)

fout = open("rmsd.byres.cym.bk.dat", "w")
for j in range(0, 374):
    sum = 0.0
    for i in range(nframe-5000, nframe):
       sel = AtomSel("backbone", molid, frame=i)
       sel.align(ref, frame=i)
       res_ref = AtomSel('backbone and residue %i' % j, refid)
       res_fra = AtomSel('backbone and residue %i' % j, molid, frame=i)
       sum = sum + res_fra.rmsd(res_ref)
    fout.writelines("%6i%8.3f\n" % (j+1, sum/5000.0))
fout.close()

>
> 2. Is it correct to say that "image" is not needed, but a rms fit is
> required for PCA?

I think you only need to superimpose for PCA analysis. This is for
removing translation and rotation.

>
> Thanks, any help/advice is much appreciated!
>
> ZT
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