Re: [AMBER] Connect atoms in a pdb created with nab

From: Jason Swails <>
Date: Thu, 18 Jun 2015 08:05:16 -0600

On Thu, Jun 18, 2015 at 7:59 AM, Jean-Patrick Francoia <> wrote:

> Got it.
> Actually, I thought about this because I'm facing an issue:
> When I build my molecule from these custom residues, sometimes the atoms
> are very close. So close that, for example, vmd or other visualization
> softwares create a bond between them.
> So it might not be a problem for Amber and its calculations, but it is a
> problem for visualizing. Do you have any suggestion to solve that ?

​VMD ignores CONECT records in PDB files and always determines bonds by
distance, so it wouldn't matter for VMD, anyway. I'm not sure if Chimera
or PyMol do the same thing or not.

If you create a prmtop file and use that to generate the topology in VMD,
then the bonds in the prmtop will be respected, so that's an option.
 (Should also work for Chimera -- not sure about PyMol.)


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jun 18 2015 - 07:30:02 PDT
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