Re: [AMBER] standard and non-standard residues

From: Ramin Ekhteiari <>
Date: Sun, 21 Jun 2015 08:37:55 +0000 (UTC)

Thank you for your advices.
But my covalently bound non-standard residue is "2-hydroxypropyl" that covalently bonded to standard residues (pyranose units). How can I find the CIF file of this residue (2-hydroxypropyl)?


     On Saturday, June 20, 2015 8:40 PM, David A Case <> wrote:

 On Sat, Jun 20, 2015, Ramin Ekhteiari wrote:

> I am trying to generate parameter and topology files for my system using
> tleap module, but the system includes standard and non-standard residues
> while these residues have connected to each other. 

The recommended way to handle this is outlined in tutorial B5.  This deals
with modified amino acids in proteins, but the principles should work for
sugars as well.

....hope this helps....dac

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Received on Sun Jun 21 2015 - 02:00:03 PDT
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