VMD-L Mailing List
From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Dec 31 2009 - 04:40:14 CST
- Next message: ÖÜÎIJý: "Superposition of Multiple Trajectory Timesteps"
- Previous message: Francesco Pietra: "sbcg with multimers"
- In reply to: Francesco Pietra: "sbcg with multimers"
- Next in thread: Anton Arkhipov: "Re: sbcg with multimers"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
I forgot to mention that it is not a homotrimer, so that your sbcg
tutorial for a homodimer requires at least a major modification (the
.psf for the trimer and all-atom reference)
francesco
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Wed, Dec 30, 2009 at 10:22 PM
Subject: sbcg with multimers
To: Anton Arkhipov <anton_at_ks.uiuc.edu>
Cc: vmd <vmd-l_at_ks.uiuc.edu>
Hello Anton:
Just a quick question. I tried your sbcg with a trimer (three
subunits, or three chains if you like) protein, created the cg pdb,
.top and .par files using "Determine bonds from all atom".
Then, in building the cg .psf file with PSF Builder, the "segments
identified" were just a line
01  1  1-  42  none  none  Other
Does that mean that "bonding" was also created between the three
chains, arriving at a sible chain? From the graphic screens it looks
like so.
If my guess is correct, what about building the sbcg model separately
for all three subunits and then combine the results? Is that possible?
Thanks and happy new year
francesco pietra
- Next message: ÖÜÎIJý: "Superposition of Multiple Trajectory Timesteps"
- Previous message: Francesco Pietra: "sbcg with multimers"
- In reply to: Francesco Pietra: "sbcg with multimers"
- Next in thread: Anton Arkhipov: "Re: sbcg with multimers"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]