[gmx-users] sasa question

[Mala L Radhakrishnan]

thank you!

On Tue, Apr 9, 2019 at 11:33 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
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-- 
Mala L. Radhakrishnan
Whitehead Associate Professor of Critical Thought
Associate Professor of Chemistry
Wellesley College
106 Central Street
Wellesley, MA 02481
(781)283-2981