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

From: David A Case <>
Date: Sun, 21 Jun 2015 11:26:37 -0400

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 - 08:30:02 PDT
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