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

From: Jean-Patrick Francoia <>
Date: Thu, 18 Jun 2015 15:59:15 +0200

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 ?


On 18/06/2015 15:47, Jason Swails wrote:
> 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).
> HTH,
> Jason

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Received on Thu Jun 18 2015 - 07:00:04 PDT
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