Dear Tom; Thank you very much for your reply and pointing out the overlap van der waals issue. One thing how much the issue is concerned if I am using one receptor against a series of small ligand. I am intrested to estimate the entropy by using the ratio between total molecular volume to van der Waals volume. As you suggested to measure the compactness which would give the compactness of surface protein, it would not estimate the changes in the inside of the protein. I would be thankful for any help. with regards, Navnit Tom Goddard wrote:
Hi Navnit,
Not sure what you mean by "vdw volume". I guess you mean the volume within the vdw surface. That's not just the sum of the spherical atom volumes since those atom spheres overlap, so the calculation is not trivial.
Perhaps the following will serve as a useful measure of "compactness". Divide the solvent excluded surface enclosed volume by the solvent excluded surface area. This gives a value with units of distance, a kind of mean radius quantifying the curvature of the surface. For a given volume a sphere will give the largest value, while a shape with many protrusions will give a smaller value. The larger the value the more sphere-like (globular) the shape.
Tom