From: Sabine Reisser (
Date: Mon Feb 18 2013 - 09:45:38 CST

Hi everyone,

I parametrized and geometry-optimized a single benzol C6H6 Ring, saved
it in a pdb-file and tried to visualize its surface within VMD (Drawing
method -> Surf). In all of my tries, the surface never completely
closed. I noticed that the amount of closing depends on the coordinates.
In the beginning, I had all z coordinates on 0 since the molecule is
planar. For this, I good the worst results, the surface contained many
individual patches which didn't fuse. Translating and rotating the
coordinates enhanced the result. It also seemed that negative
coordinates are deprecated by the SURF module. I also tried pqr
structures with different radii, which changed the surface volume as
expected but didn't enhance closing.

I suppose that there is a bug or at least some incompleteness in the
SURF code. If somebody could provide a fix or a workaround, I would be
very glad.

Thanks for reading and