15 Jan
2010
15 Jan
'10
2:11 a.m.
Hi, 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? Thanks for your help.