[gmx-users] sasa question

Justin Lemkul jalemkul at vt.edu
Tue Apr 9 17:33:26 CEST 2019

On 4/1/19 8:21 AM, Mala L Radhakrishnan wrote:
> 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?

This is correct.



Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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