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

From: Jean-Patrick Francoia <>
Date: Thu, 18 Jun 2015 16:09:19 +0200

Ok, thanks, that's what I wanted to know.

On 18/06/2015 16:05, Jason Swails wrote:
> 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.)
> HTH,
> Jason

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Received on Thu Jun 18 2015 - 07:30:03 PDT
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