[gmx-users] mutation to/from proline

[afsaneh maleki]

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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