[gmx-users] LIE using g_lie

J Peterson think_beyond at aol.com
Fri Aug 3 15:15:34 CEST 2012

Dear colleagues,

I have some doubts about LIE and would like some clarifications.

While I calculate the LIE using g_lie, it gives the DGbind energy in KJ/mol
and a standard deviation in parentheses. How well can I use this value alone
or meaningful it is by itself in comparing the binding affinity of a set of
ligands (not calculating the same for the ligand-only system) ?

Another query is that, to calculate the DGbind using the following formula
DGbind = vdw_bound - vdw_free + Elec_bound - Elec_free

Are the values calculated by -Clj tag is the value for vdw_bound or vdw_free
and -Cqq is for Elec_bound or Elec_free?

In another literature, this formula is further detailed DGbind_formula


where alpha, beta and gamma values are also needed, what are these values
and how to calculate them?


Peterson J

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