VMD-L Mailing List
From: Irene Newhouse (einew_at_hotmail.com)
Date: Thu Mar 18 2010 - 19:43:16 CDT
- Next message: Bernardo Sosa Padilla Araujo: "writepdb using selection form different molecules"
- Previous message: Nuno Sousa Cerqueira: "Re: Running IMD interactivelly under the shell"
- In reply to: Irene Newhouse: "wrapping dimer units in a Desmond traj"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
I sent this query 2 weeks ago, and not a sausage. Should I contact the pbctools developer? Desmond developer?
Thanks!
Irene
From: einew_at_hotmail.com
To: vmd-l_at_ks.uiuc.edu
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
_________________________________________________________________
Hotmail is redefining busy with tools for the New Busy. Get more from your inbox.
http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:WL:en-US:WM_HMP:032010_2
- Next message: Bernardo Sosa Padilla Araujo: "writepdb using selection form different molecules"
- Previous message: Nuno Sousa Cerqueira: "Re: Running IMD interactivelly under the shell"
- In reply to: Irene Newhouse: "wrapping dimer units in a Desmond traj"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]