VMD-L Mailing List

From: Tyler Luchko (tluchko_at_gpu.srv.ualberta.ca)
Date: Sun Nov 23 2003 - 16:18:10 CST

Hello,

I've written a script to set all atom radii to their CHARMM 27
Lennard-Jones radii and have run into a problem with MSMS. Unless I set
the probe radius quite large, typically > 2, MSMS returns no surface. I
have run MSMS on the same structures myself using CHARMM radii without a
problem. I suspect that with VMD the problem lies in that many of the
hydrogens have radii so small that they are completely buried inside
another atom. Would it be possible to screen for such atoms and not
submit them?

Thank you,

Tyler

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