VMD-L Mailing List

From: Sebastian Maximilian Wilhelm (Sebastian.Wilhelm_at_rwth-aachen.de)
Date: Wed Mar 16 2011 - 12:40:43 CDT

Hello,

I want to calculate the van-der-Waals area of a molecule and to compare it with the literature value (for example BONDI). At the moment, I am using

measure sasa 0.0 $resid xy,

with 'resid xy' the molecule to be analyzed. If this molecule is a sphere (like for argon), I receive exact one value for all frames of the MD simulation for the loaded .pdb-file, which I can reproduce by A=4*pi*r**2 by hand (r is the chosen vdW-radius).

But if this molecule doesnīt have a perfect sphere shape (like for propane), I receive for all loaded frames nonconstant values, which are in the same order like the one from BONDI, but may also vary up to 5 Angstroem*Angstroem. All intramolecular bonds and angles of the investigated molecule are constant for all frames, so the molecule canīt change its molecular form. If only one site (for example the CH3 site) of propane is analyzed, all is fine and I get only one result (the expected one) for all frames.

I donīt understand why I receive different values (i.e. one value for each different frame, but never the same), if a complete molecule is investigated, and not only one. Like said before, for perfectly sphere shaped molecules or sites I get just one result. Is SASA with an extended radius of 0.0 inappropriate to calculate the surface of whole molecules? Does there exist a better method for calculating the vdW-area?

Thank you very much for your help!

Best regards,
Sebastian