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



 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
 tel. +420 541 129 508
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