Subject: RE: summary for program for superimposing (small) molecules and new question

From: "Mark Mackey" <m.mackey_at_cresset-bmd.com>
Date: Fri, 8 Aug 2003 08:50:15 +0100

Umm, how did you align the two molecules? If you take a molecule and an
exact copy which you translate by 5A, then your Excel method will give
you an RMSD of 5A, which is obviously incorrect.

The standard molecular alignment methods give you the _minimum_ RMSD
i.e. they rigidly rotate and translate the molecules so as to give the
smallest possible RMSD for those two structures. This is the standard
method of determining how 'close' two structures are. Simply calculating
the differences of the input coordinates gives you no useful information
whatsoever.

-- 
Mark Mackey
Cresset Biomolecular Discovery

-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request_at_ccl.net] On
Behalf Of Dr. Richard L. Wood
Sent: 07 August 2003 20:58
To: Dr. Daniel Glossman-Mitnik
Cc: chemistry_at_ccl.net
Subject: 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, 
Richard 
  
> From Jason D. Gans: Hello, 
Qmol, available from the CCL software repository 
http://www.ccl.net/cca/software/MS-WIN95-NT/qmol/index.shtml 
can superimpose molecules and compute RMS deviation. 
Regards, 
Jason Gans 
B division 
Los Alamos National Lab 

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