[gmx-users] LIE

[Ghermes Chilov]

Hi!

AWSdS>         I did some tests trying to evaluate Linear Interactive Energy
AWSdS> method to obtain estimatives of free bind energy between protein and
AWSdS> ligand.

AWSdS>         I tried using Reaction Field, Cut-off and PME, with and without
AWSdS> ions or neutralising proteins (by protonation or deprotonation of some
AWSdS> residues)....

AWSdS>         First, using PME under any circumstance gave EE very different
AWSdS> (about half) from RF and Cut-off options.  Should I not expect EE at close
AWSdS> values independently of the electrostatic treatment?

By the way, may i take an interest in why at all have you tried PME? I
think that when you try to compute an interaction energy you
do not need to account for the periodic images of the protein - it
looks as if you model very concentrated solution, isn't it? IMHO PME
is adequate in simulating solutions of small molecules, when you can
take a box big enough to adjust the concentration of the solute to a
realistic value. Hm?!

Ghermes Chilov

PhD student
Moscow State University