Re: [AMBER] Load "library" of custom residues

From: Jean-Patrick Francoia <>
Date: Sun, 21 Jun 2015 17:43:50 +0200

Hello, thank you for your answer.

Is there a better solution ? Because there are 6 residues in this pdb
file. And the .bnd file contains all the infos about the bonds of all
the residues.

I saw this tutorial, and I wondered if there was a better solution. What
are the .bnd files made for ? I got an example of a bnd file from

In this folder, each pdb file describes several residues, and there is a
bnd file next to each of them to describe the bonds within the residues.
I thought amber or xleap would use these files to identify the residues
of a molecule. Basically, I'm trying to tweak that, and add new residues
this way.

Could you enlighten me on how Amber/xleap uses the files in /dat/reslib ?

On 21/06/2015 17:26, David A Case wrote:
> On Sun, Jun 21, 2015, Jean-Patrick Francoia wrote:
>> I have a folder containing informations about custom residues:
>> lysine42/
>> lysine42.bnd (contains informations about the bonds within the
>> custom residues)
>> lysine42.pdb (contains informations about the custom lysine residues)
>> lysine42.chi (empty)
>> lysine42.qr (empty)
>> Someone gave me this folder.
>> I would like to know if it is possible to load the folder in xleap.
>> Finally, I would like to load a molecule built on these custom residues
>> in xleap, to generate the prmtop and the inpcrd files.
> You can follow the lead of tutorial B5 to generate Amber libraries for
> modified resiudes. Of the files listed above, only the PDB file will be of
> much help, and you will have to add capping groups to the N- and C-termini
> of your lysine; many modeling programs (including xleap) can assist you
> in doing this. After that, the procedure is pretty straightforward.
> ....good luck....dac
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Received on Sun Jun 21 2015 - 09:00:03 PDT
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