VMD-L Mailing List
From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Mon Jun 23 2014 - 15:48:01 CDT
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.
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Can’t you just define them as a residue and add it to your topology file?
From: owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu> [mailto:owner-vmd-l_at_ks.uiuc.edu] 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?