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PostPosted: Mon Feb 02, 2015 10:46 am 
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Joined: Mon Feb 02, 2015 10:44 am
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Why Autodock gives Different RMSD values for same docking? Which RMSD to take and why?

when i did docking with autodock (using command mode), I got one set of RMSD values (referred to as refRMS) in protein.dlg file under RMSD Table section. There is also a python program in AutoDock Tools ("compute_rms_between_conformations.py") in Utilities folder which gives RMSD values. These values differ. (e.g. between ligand.pdbqt and ligand_1.pdbqt, RMSD using python code gives value as 2.9117 and refRMS in protein.dlg file has value of 1.67).

Can someone please help me to know why these values differ and how both these values are calculated?


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