[phenixbb] N-acetylgalactosamine lacking amide planarity restraint

Tristan Croll tristan.croll at qut.edu.au
Wed Jan 20 11:34:12 PST 2016

Hi Nigel,

Actually, this may have been due to a mistake on my part leading to a bad input structure. I will double-check tomorrow and let you know. I do know that many older structures containing N-acetyl sugars have the amide bond badly twisted suggesting that at some point the restraint libraries didn't cover it. If this case turns out to be my fault I apologise for the false alarm.

Best regards,


From: Nigel Moriarty <nwmoriarty at lbl.gov>
Sent: Thursday, 21 January 2016 5:28 AM
To: Tristan Croll
Cc: phenixbb at phenix-online.org
Subject: Re: [phenixbb] N-acetylgalactosamine lacking amide planarity restraint


Can you send the model so I can check what is happening.



Nigel W. Moriarty
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Lawrence Berkeley National Laboratory
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Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
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On Mon, Jan 18, 2016 at 5:19 AM, Tristan Croll <tristan.croll at qut.edu.au<mailto:tristan.croll at qut.edu.au>> wrote:


I'm refining a structure that includes an O-linked N-acetylgalactosamine (NGA) residue, and from the way it's behaving the N-acetyl amide clearly has no restraints on its planarity. It's currently twisted almost 45 degrees from planar despite having no close contacts.



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