Re: CCL:summary for program for superimposing (small) molecules and new question

I have a question as to how the program QMol calculates the RMSD of two structures.

I used Excel to calculate the RMSD for two different conformations of the same molecule and compared the result that I get using QMol, and I get two different values, and I am wondering why that is.

In Excel, I calculated the distances between the same two atoms in the two conformations, squared them, added them up, then divided by the number of atoms.
After this, take the square root to get the RMSD.

It looks to me like QMol does something different.

Thanks in advance,

From Jason D. Gans: Hello,

Qmol, available from the CCL software repository

can superimpose molecules and compute RMS deviation.


Jason Gans

B division
Los Alamos National Lab 

Richard L. Wood, Ph. D.
Physical/Computational Chemist