From chemistry-request(+ at +)ccl.net Thu Aug 7 15:57:40 2003 Received: from postoffice.mail.cornell.edu (postoffice.mail.cornell.edu [132.236.56.7]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h77JveNG013687 for ; Thu, 7 Aug 2003 15:57:40 -0400 Received: from cornell.edu (cs666981-224.satx.rr.com [66.69.81.224]) by postoffice.mail.cornell.edu (8.9.3p2/8.9.3) with ESMTP id PAA27013; Thu, 7 Aug 2003 15:57:39 -0400 (EDT) Message-ID: <3F32AF2F.110FE643-.at.-cornell.edu> Date: Thu, 07 Aug 2003 14:57:35 -0500 From: "Dr. Richard L. Wood" Organization: Cornell University X-Mailer: Mozilla 4.5 [en]C-CCK-MCD {TLC;RETAIL} (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: "Dr. Daniel Glossman-Mitnik" CC: chemistry-.at.-ccl.net Subject: Re: CCL:summary for program for superimposing (small) molecules and new question References: <002a01c35d09$9d6a63f0$8400000a \\at// laquicom02> Content-Type: multipart/alternative; boundary="------------735E08B5D339FC9B98749EAE" --------------735E08B5D339FC9B98749EAE Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit 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 --------------735E08B5D339FC9B98749EAE Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit 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
 
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