[Chimera-users] calculation of volume
goddard at cgl.ucsf.edu
Thu Aug 14 11:13:06 PDT 2008
I don't have any further advice. Entropy is a statistical property
regarding the number of available conformations, quantum states or
classically the accessible volume of phase space (position and momentum
coordinates of ligand, receptor, solvent and ions). I imagine you can
get some estimate from an MD trajectory. Comparing the "vdw volume"
versus the volume of a solvent excluded surface says something about the
entropy effects due to solvent exclusion. The difference in volumes is
just from the nooks where the water molecules can't reach. But it
doesn't include entropy from motion confinement of ligand and receptor.
As mentioned before the closest you'll get to the vdw volume in the
current Chimera is a solvent excluded surface with small probe radius
(0.5A minimum allowed, default is 1.4A).
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