[gmx-users] two question about calculating the binding free energy using g_lie method

zjim fit_tone at 163.com
Thu Dec 23 11:55:40 CET 2004

Dear all
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?;)
Following is my two quesiton about g-lie.
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?

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:
PME:Coul-SR(rcoulomb=0.9):          -278.337kj/mol
PME:Coul-SR(rcoulomb=1.2):          -303.292kj/mol
Cutoff:Coul-SR(rcoulomb=1.2):       -509.506kj/mol    
gromacs 3.1.4(sigle)
Is that reasonable .

please give some advice
thank you very much
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