Dear All
I have some query about rmsd calculation. If I just translate/transform coordinates of some structure (keeping internal coordinates same) then calculating like this does not make sense?
(In brief I have residues 1 to 20 and I simulated keeping 1-10 residues with fixed internal geometry, rigid body, using EMAP)
rms reference mass :1-10 out test.rms
this will give wrong impression that structure has changed much though it just translated
to avoid this do I need to use like this or something else?
rms reference mass :1-10 out test_fit.rms fit
(I used ''fit'' here and I think nofit is default)
But using fit gives same output (test.rms and test_fit.rms are same). I mean using fit rms graph should be almost flat
thanks
Jiom
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 20 2014 - 16:00:04 PST
