VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Jan 26 2015 - 11:30:46 CST

Hi Charles,

You are on the right track, but I think you dehydrated trajectory may
have another resid 48 somewhere that isn't part of the protein. Would
replacing the res selection text by: "protein and resid 48" solve your
problem? SASA needs the restrict selection to be a subset of the initial
selection, and I think your selections may have been too loose.

-Josh Vermaas

On 01/25/2015 11:31 PM, Charles McAnany wrote:
> 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.