[gmx-users] Re: Linear Interaction energy calculations

[J Peterson]

Dear colleagues,

Thanks for opening up this topic. I also 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 we use this value
alone or meaningful it is by itself, not calculating the same for the ligand
alone, in comparing the binding affinity of a set of ligands?

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 
http://gromacs.5086.n6.nabble.com/file/n4999924/DGbind.jpg 
where alpha, beta and gamma values are also needed, what are these values
and how to calculate them?

Thanks,

Peterson J





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