Gmx sasa question

User discussions
1

Dear all,

I am trying to obtain the sasa of a protein that is squished in the middle of a protein complex.
For example to visualize:
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If I run gmx sasa on the docked complex and using the middle protein as a reference through -n index.ndx, will it take into account that no solvent is accessible at the binding interfaces of the middle protein? The reason I ask is that I notice that the sasa does not decrease when I pull apart the 2 proteins surrounding the middle protein and sometimes I see the sasa decrease when I do so.

2

what is middle of a protein?

3

Sorry if my explanation was unclear.

Imagine 3 actin protein monomers that are polymerized. So there are 3 proteins strung together in a line (kind of like a train). The middle protein is the protein that is in between the other proteins.

So protein 1-protein2-protein 3. I’m interested in the sasa of protein 2.

Hope that helps.