From: Irene Newhouse (
Date: Thu Mar 18 2010 - 19:43:16 CDT

I sent this query 2 weeks ago, and not a sausage. Should I contact the pbctools developer? Desmond developer?




Subject: vmd-l: wrapping dimer units in a Desmond traj
Date: Tue, 2 Mar 2010 09:51:25 -1000

I've got Desmond trajectories in which one of the monomer units of a dimeric protein wraps. I can still align on each monomer & get backbone RMSD values for each monomer, but I'd also like to analyze whether the dimer is stable or drifting apart.
So I found the web references to the pbctools plugin. I used the initial frame to determine values for a, b, & c, using the measure minmax command, and set the cell with pbc set "64.4 96.3 99.2" -all . Note that the use of "" is not shown in the documentation, but not using "" resulted in pbctools errors. Then I pbc wrap -sel "protein or resname HEM or resname ACT" -all . The result is disappointing - VMD does a lot of work, but the dimer is not reconstituted. Instead, there are anywhere from 2 to 4 segments of protein. They are distributed differently from the original, but they're still not in closest proximity. Frame 0 contains the unwrapped protein, while most of the other frames are wrapped; I don't know if this might be contributing.
Thanks for your help!
Irene Newhouse

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