Re: [Chimera-users] calculation of volume
Hi Navnit, Sorry, I don't know of a way to calculate the van der Waals volume in Chimera. You can see the VDW volume, of course, by simply displaying the atoms in the sphere representation, but that does not give the volume value. In theory, you could get values closer to the VDW volume by calculating molecular surface with smaller and smaller probe radius. In practice, this tends to increase the number of surface calculation failures, and currently the smallest allowed probe radius value is 0.5 angstroms. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 14, 2008, at 7:01 AM, Navnit Kumar Mishra 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
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, 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). Tom
participants (3)
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Elaine Meng -
Navnit Kumar Mishra -
Tom Goddard