From: Irene Newhouse (
Date: Fri Jul 13 2007 - 16:47:05 CDT

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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