VMD-L Mailing List

From: Charles McAnany (vmdnamd_at_charlesmcanany.com)
Date: Sun Jan 25 2015 - 23:31:38 CST

Friends,
I am trying to see how buried a particular residue is during some
simulations. I have dehydrated trajectories, and what I want to know is:
"How much surface area of residue 48 is exposed to solvent?" Clearly, this
is a sort of SASA problem, but I'm not too clear on how to use measure sasa
in this situation, or if measure sasa is even the right tool. I was hoping
to use:

set protein [atomselect top protein]
set res [atomselect top "resid 48"]
measure sasa 1.4 $protein -restrict $res

but vmd balks: invalid first atom selection.

I believe this is because the trajectory is dehydrated and therefore
$protein is the entire molecule, but I feel like it shouldn't be necessary
to load twenty different 30-gigabyte (hydrated) trajectories every time I
want to tweak my analysis script.

If anyone has any other ideas for capturing how buried a particular residue
is other than SASA, I'm all ears. I am interested in the relative
differences in buriedness between trajectories more than the exact
buriedness for a single trajectory. If I could measure, for example, the
area on a quicksurf representation "due to" residue 48, I'd settle for that.

Sincerely,
Charles McAnany,
Mura Lab, University of Virginia.