Dear all, sorry for off topic question. My protein is composed to two domains connected by a flexible linker and shows large domain motion with large RMSD value of 9.0 A* difference with respect to the initial structure, when simulated for 20 ns. As the first domain doesn't shows any RMSD change when superimposed to initial structure but the other domain moves significantly. so my question is how i could be to calculate the angle of motion in degree of the flexible domain with respect to the initial structure after superimposition. thank you all in advance
Regards *Rajan kumar choudhary* *Senior Research Fellow* *Department of Atomic Energy(Govt.Of India)* *ACTREC TATA Memorial Center * *Kharghar Navi-Mumbai* *Mumbai-410210* *India*
