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<p class="MsoNormal">Hi,<br></p><p class="MsoNormal">I want to calculate relative free energy associated to
mutation of P1 (native protein) to p2 (mutated protein).In this mutation, <span style=""> </span>Isolusine (in P1) is mutated to Proline(in P2).
With using Thermodynamic cycle:</p>

<p class="MsoNormal"><span style="">                </span>Bilayer+P1=
= =&gt; Bilayer-P1<span style="">  </span><span style=""> </span><span style=""> </span><span style="">              </span><span style="">      </span><span style=""> </span><span style=""> </span>delta G1 (association P1)</p>


<p class="MsoNormal"><span style="">                </span>Bilayer+P2=
= =&gt; Bilayer-P2<span style="">  </span><span style=""> </span><span style="">  </span><span style=""> </span><span style="">        </span><span style="">        </span><span style="">     </span>delta G2 (association P2)</p>


<p class="MsoNormal"> </p>

<p class="MsoNormal"><span style="">  </span><span style=""> </span>Where <span style="">   </span><span style="">   </span><span style="">          </span>P1 = = =&gt; P2 <span style="">    </span><span style="">          </span><span style=""> </span><span style="">  </span><span style=""> </span><span style="">            </span><span style="">  </span><span style="">  </span><span style="">  </span><span style=""> </span>deltaG3</p>


<p class="MsoNormal"><span style="">               </span><span style="">              </span><span style=""> </span><span style=""> </span><span style="">  </span>Bilayer-P1 = = = &gt; Bilayer-P2<span style="">  </span><span style=""> </span><span style=""> </span><span style=""> </span><span style=""> </span><span style="">  </span>deltaG4</p>


<p class="MsoNormal">So, delta deltaG= (delta G1(association P1)- deltaG2 (association
P2))= (deltaG3- deltaG4)</p>

<p class="MsoNormal">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.</p>

<p class="MsoNormal">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? <span style=""> </span>I searched but I didn’t
find! Or is there manual for mutating from/to proline?</p>

<br clear="all"><br>I appreciate your help,<br>Afsaneh <br><br>