VMD-L Mailing List

From: Daniel Klose (daniel.klose_at_uni-osnabrueck.de)
Date: Mon Aug 27 2012 - 03:22:04 CDT

Dear VMD users and developers,

as previously discussed on this mailing list, wrapping protein complexes that cross periodic boundaries in the course of a longer MD trajectory can be wrapped into a single unit cell using vmd package pbctools and the commands "pbc unwrap" or "pbc wrap -compound fragment -center com -centersel "name CA" -all"

as discussed in http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/19108.html

Now having a two chain protein complex (2 fragments) in my trajectory the complex also crosses the pbc cell boundaries and now I'd like to wrap the complex together, so that both fragments / chains are either wrapped or not wrapped, but keeps occuring that only one is wrapped and the other is not.

I also tried "pbc join res -sel protein -ref protein", after reading the unit cell from different .xst files from the various trajectory steps.

I could sometimes get the individual chains wrapped correctly (without bonds streching over the whole cell), but never the two chains together so far... so I wonder what I did wrong?
The trajectory is shed of any waters by catdcd if that matters...

Any help or suggestions with this pbc wrapping problem will be greatly appreciated!!
Thank you!!

Best wishes,
Daniel