From chemistry-request: at :ccl.net Thu Aug  7 16:52:31 2003
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Message-ID: <3F32BBF3.1060002=at=chemi.muni.cz>
Date: Thu, 07 Aug 2003 22:52:03 +0200
From: Lubos Vrbka <shnek=at=chemi.muni.cz>
Reply-To: shnek=at=chemi.muni.cz
Organization: NCBR
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To: "Dr. Richard L. Wood" <rlw28=at=cornell.edu>
Cc: chemistry=at=ccl.net, daniel.glossman=at=cimav.edu.mx
Subject: Re: CCL:summary for program for superimposing (small) molecules and
 new  question
References: <002a01c35d09$9d6a63f0$8400000a#* at *#laquicom02> <3F32AF2F.110FE643=at=cornell.edu>
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Dr. Richard L. Wood wrote:

> 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.

isn't it possible that QMol produces for example mass-weighted RMS or 
something similar? i can remember having similar problems (i.e. 
different values of the RMSD on the same set of structures) with some 
other programs (e.g. amber/ptraj, amber/carnal and vmd). maybe qmol 
could be some kind of similar case...

regards,
lubos

-- 
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Mgr. Lubos Vrbka
National Centre for Biomolecular Research
Masaryk university, Brno, Czech Republic

shnek=at=chemi.muni.cz
http://www.chemi.muni.cz/~shnek
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