[gmx-users] two question about calculating the binding free energy using g_lie method
fit_tone at 163.com
Thu Dec 23 11:55:40 CET 2004
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:
Is that reasonable .
please give some advice
thank you very much
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