From: Irene Newhouse (
Date: Thu Jul 26 2007 - 17:40:01 CDT

This just showed up in my mailbox. I'm not sure how or why, because it's an issue that was already settled for me by the kind people on this list. So please ignore it - it's a ghost message.

Oddly enough, that's the kind of day I'm having today! A day where you say, "Typical!" when something like this happens.


> From:
> To:
> Subject: vmd-l: puzzling psfgen problem with deleted atoms coming back
> Date: Fri, 13 Jul 2007 11:47:05 -1000
> I'm working on mods to the CHARMM topology file to be able to use oliogosaccharides in NAMD runs. I've attached the modified topology files, the psfgen command file & the pdb file I start from. What I observe is that in the pdb file created by VMD 1.8.6, linking of saccharides 1 & 2 works just fine. That's a patch I wrote myself. Linking saccharide 3 to 2 uses another patch I wrote myself, and that's the one that has the problem, & I can't seem to find it. What I observe is that atoms on sacch. 3 which are deleted in the patch process "come back" - they're given coordinates of 0, 0, 0 & an occupancy of -1 in the pdb file generated by psfgen. Linking sacch. 3 to 4 uses the same patch & causes the same problem, while linking 5 to 4 uses a patch that's part of the CSFF material & works just fine.
> I could write a sed script that deletes all entries with -1 occupancy from the pdb file, but I'd rather know what embarrassing mistake I've made this time. I've attached my modified topology file, my command file for psfgen [which I use from the VMD Main window] & my initial pdb file.
> Thanks so much!
> Irene Newhouse
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