Weird Bond In Non-Polar Tail

From: Danielle Grodi (
Date: Thu Jun 18 2015 - 10:15:53 CDT


I've been working with a detergent, DDM which has a 12 carbon-long non
polar tail. I've built this structure using Avogadro. After I run the pdb
file through psfgen, then load the psf file in and the pdb file into the
psf file, two bonds that I explicitly created are now missing.

Is there any easy way to recreate these bonds? Does anyone have an idea
about how to fix this?

Thank you,

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