[AMBER] symmetry corrected RMSD calculation

From: Pooja Khurana <btpooja.yahoo.in>
Date: Sun, 20 Mar 2011 08:08:21 +0530 (IST)

Hi all,

When I superimposed two complexes, I get the rmsd value of 1.7 but the two complexes exactly overlay on each other. I found out that because of the symmetry in the ligand, the atom say C1 which is on the left in one complex is on the right in the other complex but the other atom C11 is on the left side, that is exactly at the same position as C1, similarly is the case with the other atoms in the ligand. So that is why the rmsd is high.

But I want to compute the actualy rmsd which should be somewhere around 0, is there any way to do so? Because VMD measures the rmsd on atom-atom correspondence basis, so it is giving 1.7 only.

Is there any other tool available to do so, and I have several such complexes so I want a command line interface for doing that?

I found out that there are some softwares that does calculate symmetry corrected RMSD but I am not able to access them? Can you suggest me some other that any one must have used?

ANd please also tell me that how these software compute such an RMSD? As VMD uses Kabsch's algorithm to align two macromolecules, and then one one-to-one basis is computes the RMSD using the standard formulae. But what if the molecule has symmetry and the symmetrical atom does not have one-to-one correspondence in the coordinate file?

Please suggest me some good tool and the algorithm behind this. I shall be really grateful to you..

Thanks in anticipation,

B.E. Biotechnology

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Received on Sat Mar 19 2011 - 20:00:02 PDT
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