[gmx-users] sasa question

[Mala L Radhakrishnan]

Hi all,

I wanted to double check something which I believe is true based on doing
my own tests, but --

When I use gmx sasa to calculate the SASA of a group within a larger system
(by selecting the number corresponding to that group from the interactive
menu upon running), it will output the SASA of that group assuming all the
other components in the system are NOT there, correct?  In other words, if
I have a binding complex and I choose one partner from the menu, it will
compute the surface area of that one partner assuming it was essentially
not bound to the other partner, which it technically is in the structure
file).  This seems to be what I observe, since SASA of partner 1 + SASA of
partner 2 is greater than the SASA of the complex via this process but I
wanted to double check with someone who knows for sure.

I presume, then, that for me to get the SASA of "just the part" of a
partner that is solvent-exposed upon binding, I would need to choose the
complex as the group but then output each atom's SASA and then sum over the
atoms in the relevant binding partner.  Yes?

Thanks so much!

Mala

-- 
Mala L. Radhakrishnan
Whitehead Associate Professor of Critical Thought
Associate Professor of Chemistry
Wellesley College
106 Central Street
Wellesley, MA 02481
(781)283-2981