Hi, I want to calculate relative free energy associated to mutation of P1 (native protein) to p2 (mutated protein).In this mutation, Isolusine (in P1) is mutated to Proline(in P2). With using Thermodynamic cycle:
Bilayer+P1= = => Bilayer-P1 delta G1 (association P1) Bilayer+P2= = => Bilayer-P2 delta G2 (association P2) Where P1 = = => P2 deltaG3 Bilayer-P1 = = = > Bilayer-P2 deltaG4 So, delta deltaG= (delta G1(association P1)- deltaG2 (association P2))= (deltaG3- deltaG4) To define the B state that will be used for the free energy calculation. For this; I need to specify the new atom type of each mutated atom and the set of parameters to it. But my question is that with regarding to special structure of proline, is it possible to update topology file? Who was done mutation of proline before? I searched but I didn’t find! Or is there manual for mutating from/to proline? I appreciate your help, Afsaneh
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