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Hello,
Has someone been able to successfully apply the LIE
method for estimation of binding free energies using the GROMOS96 simulation
package?
I am studying the binding of some charged
ligands to enzyme receptors but it seems there´s a problem with the
description
of molecular interactions (specially electrostatic) since the results are
nowhere near the experimental ones.
I am using solvated spheres with the extended wall
boundary condition and a 17 A cut off radius for long range non bonded
interactions. A reaction field correction is applied to account for
the missing electrostatic contributions outside the sphere.
I could not find any papers where something like
this was attempted (i.e., LIE combined with GROMOS96).
I am aware the Q program is out there but I just
would like to make it right using GROMOS96.
Any pointers will be greatly
appreciated.
Thanks,
F.
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