From: Tristan Croll (
Date: Mon Jun 23 2014 - 15:48:01 CDT

Hi Richard,

No, it's not that. The glycans have topologies and build just fine. It's just that AutoPSF gets mixed up about the *type* of residues they are, and wants to apply NTER and CTER patches to them.



Tristan Croll
Faculty of Science and Technology
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443

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On 24 Jun 2014, at 4:35 am, "Richard Wood" <<>> wrote:

Can’t you just define them as a residue and add it to your topology file?


From:<> [] On Behalf Of Tristan Croll
Sent: Saturday, June 21, 2014 7:14 PM
Subject: vmd-l: Minor bug/annoyance: AutoPSF and acetylated CHARMM glycans

This is a very minor problem since I suspect anyone working with CHARMM-36 glycans will usually be using their own psfgen scripts anyway, but the heuristic that AutoPSF uses to determine chain type (protein/nucleic/other) gets mixed up when it encounters N-acetylglucosamine residues (and, I suspect, other N-acetylated sugars). It designates them as protein and attempts to apply N- and C-terminal patches accordingly. I suspect the problem here is that the N-acetyl amide has atoms named N, HN, C and O, which get mistaken for backbone atoms.

On a related note, may I ask if glycans are likely to be put on the “to-do” list to be automatically handled in a future release of VMD?