Hi,<br><br>I want to calculate the RMSD between two mol2 structures in place. The two structures are different forms of the same structure. I haver modified the mol2 so that the two of them have the same serialNumber in their respective atoms. The problem is that when I use the command rmsd #model1 #model2, it return an incorrect value of the rmsd, as the value showed is too high, about 5, when it should be about 1 (the two structures are very similar). Is there any way to calculate the RMSD value in place correctly or I am doing anything wrong?<br>
<br>Thanks for your help.<br><br><br><span style="color: black;"><div dir="ltr"><div><div style="text-align: center;"><img src="http://farm5.static.flickr.com/4045/4194316803_f773f9c017_o.jpg" border="0"></div></div></div>
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