<br>Dear all<br>Now i am trying to calculate the binding free energy of protein and ligand, I prefer to use the g_lie method as my system is very big and calculating the free energy by 'slow glow' or "perturbation" is a rather rough task,is that so?;)<br>Following is my two quesiton about g-lie.<br>No1:<br>When calculated the energy of interaction, i found that the Coul-SR(ligand--ligand) has a difference of about 30kJ/mol between free in water and binding with protein. i think this difference may due to change of conformation of ligand.Is the g_lie method still suited when the conformatin change of ligand is rather large when it binding with protein?<br><br>No2:<br>for the ligand in my system has +1 charge, the PME and Cutoff method was respectively used to calculate the Coul interaction. however, the difference of the result is huge:<br>PME:Coul-SR(rcoulomb=0.9): -278.337kj/mol<br>PME:Coul-SR(rcoulomb=1.2): -303.292kj/mol<br>Cutoff:Coul-SR(rcoulomb=1.2): -509.506kj/mol <br>gromacs 3.1.4(sigle)<br>Is that reasonable .<br><br>please give some advice<br>thank you very much<br><br><br><br>
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