From: Eric Smoll (
Date: Thu Jan 08 2015 - 15:49:09 CST

Hello VMD users,

As discussed in the VMD FAQ section, when I provide a coordinate file
without a PSF file, bonding is computed with a distance search. Is there a
way to write this connectivity to file? If not, is anyone aware of a tool
to do so?

How is the distance search done? Is there a hardcoded distance cutoff for
bonding that applies to all nuclei? Does the distance search take the VDW
radius of each atom into account?