VMD-L Mailing List

From: Josh (vermaasj_at_msu.edu)
Date: Wed Nov 22 2023 - 11:20:46 CST

Hi Kevin,

I think that measure SASA might not do quite what you want, since
something like glycine is naturally going to have a smaller SASA than a
larger residue. Have you considered just selecting residues that are
close to water? If you wanted one atom per residue, a selection like:

protein and name CA and same residue as (within 3.0 of water)

Would identify residues for you with alot less fuss.

-Josh

On 11/21/23 7:08 PM, Kevin Lin wrote:
> Hello,
>
> I currently have a simulation of a protein in a waterbox. I'm looking
> to identify residues on the protein surface throughout the simulation
> using the measure sasa command. I am aware that the sasa command
> returns a surface area value for each selection I input it, which I'm
> currently giving residues. So far, I'm seeing values between 300 and
> up to over 1000. Is there a suggested threshold for a sasa cutoff
> value to identify which residues are on the surface, or is there a
> better way to do this?
>
> Any tips would be greatly appreciated!
>
> Thanks! 

-- 
Josh Vermaas
vermaasj_at_msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io