[gmx-users] g_sas => protein and ligand aggregate interface area ?

[Chih-Ying Lin]

HI
As David said,
=> How to compute protein-protein interface area?
"If you have protein A and B in complex you do three g_sas:

AB AB
A A
B B

the interface is now A + B - AB"



I want to calculate protein and ligand aggregate (small micelle of ligand)
interface area.
Is it the same step as calculation of protein A and B interface, which David
mentioned above?
But replacing protein B to Ligand aggregate (small micelle of ligand) ?

g_sas -n ligand-micelle-index.ndx ........ ?

where ligand-micelle-index.ndx includes all the atom numbers of ligand
micelle, which attached on the protein .

Is my idea correct?

Thank you
Lin
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