VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Dec 31 2009 - 04:40:14 CST

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