From: Narender Singh Maan (nsmaan_at_gmail.com)
Date: Fri Sep 28 2007 - 14:21:21 CDT
I am trying to calculate the binding free (BFE) energy by Linear Interaction
method (LIE) of a set of ligands with my protein of interest. Now in LIE all
we need from the simulations is 1) vander Waals interaction energies (VDW)
and 2) electrostatic interaction energies (ELEC) difference of the bound
ligands from their unbound form:
[DeltaG = constant1(VDW energy difference of bound and unbound form) +
constant2 (ELECT energy difference of bound and unbound form)].
To accomplish this i have already finished MD (by NAMD) simulations of all
the bound and unbound forms. But now the questions i have are
1) does the BFE here depends on how big the water box is (as long as the
bound and unbound ligands are fully solvated, while keeping all the cutoffs
and other parameters same in all the simulations)?
2) should i just extract the VDW and ELECT values from the simulation
output files to calculate the free energy by LIE method? Or do I need to
further process the extracted energies by some script etc?
3) and my last question is that which one of the following two methods is
more appropriate: a) building a separate waterbox of the same cutoff (e.g.
15 Ang from the surface) for each ligand system simulation or b) to just
delete the protein from the protein-ligand complex system and keep the same
waterbox (minus protein) to do the simulations for ligands (with new psf
Any suggestion/comment/help would be greatly appreciated.
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