Re: Weird Bond In Non-Polar Tail

From: Axel Kohlmeyer (
Date: Thu Jun 18 2015 - 10:45:06 CDT

On Thu, Jun 18, 2015 at 11:15 AM, Danielle Grodi
<> wrote:
> Hello,
> 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?

please have a look at the psfgen manual and tutorials and try to
understand how it works.

what psfgen does is primarily matching the names of residues and atoms
in your pdb file with a database of residues (i.e. the topology
file(s)) and then follows the information about bonding topology, atom
types, missing atoms and how to connect residues given in the topology

so psfgen is not aware of those extra bonds. to introduce bonds you
have two options: you create a modified residue with a new name or you
add/use a patch (e.g. what is done to introduce sulfur-bridges). not
sure what is the better choice in your specific case. there should be
sufficient documentation and tutorials to explain the process.



> Thank you,
> Danielle

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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