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 Elaine;
Thank you for so detailed description. I am interested in measuring the compactness of the complex during the simulation, I think the calculation of the ratio of molecular volume to van der waals volume provides the compactness. I have tried the procedure as you suggested to calculate the molecular volume, the value in replylog file is in two digits precision, for these calculation can I get the value in four digits precision. I am using latest chimera version 1.2540. I can calculate the total van der waals volume using the van der Waals radii for each atom excluding the hydrogen atoms. Is there a way in chimera to calcualte the van der waals volume. I would be thankful to you for any suggestions.
with regards, navnit
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,
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
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