From: Josh Vermaas (
Date: Thu Jan 08 2015 - 16:45:32 CST

Hi Eric,

The short answer is yes, you can write this out to a file. This needs to
be done in 2 steps:

1.) Trick VMD into thinking you've changed the bondlist somehow (by
default, it won't write out guessed bonds). This is the command I'd use,
which flips a switch telling VMD that the bonds should be written out to
file: mol dataflag top set bonds
2.) Write out a file with your favorite format that has bond
information. Ex: [atomselect top "all"] writepsf test.psf

The distance search takes into account the radius (see the manual:

-Josh Vermaas

On 01/08/2015 03:49 PM, Eric Smoll wrote:
> 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?
> Best,
> Eric