[Chimera-users] calculation of volume

Tom Goddard goddard at cgl.ucsf.edu
Thu Aug 14 11:13:06 PDT 2008

Hi Navnit,

  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).


More information about the Chimera-users mailing list