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

From: Jason Swails <>
Date: Thu, 18 Jun 2015 07:47:29 -0600

On Thu, Jun 18, 2015 at 2:31 AM, Jean-Patrick Francoia <> wrote:

> Hi,
> I'm just starting to use nab, and I have a naive question.
> I would like to build a molecule from custom residues. Theses residues
> are lysine-based, but it doesn't matter. They are defined in a folder of
> my project, and don't contain informations about how the atoms are
> connected (no CONECT fields) to each other.
> My nab script uses these residues to create the final molecule. It
> generates a pdb, of course also without CONECT fields. I would like to
> know if by adding CONECT fields in the definition of my custom residues,
> the final molecule generated with the nab script will include CONECT
> fields too.
> Is it possible to do that ?

​NAB will not print CONECT records.​ This should not matter for Amber,
though, since bond information is stored in the residue library file (e.g.,
the OFF libraries or mol2 files).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Jun 18 2015 - 07:00:03 PDT
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