[gmx-users] Calculating Contact Surface Area in one Graph

[Justin Lemkul]

On Tue, Dec 18, 2018 at 2:34 PM Sebastian Muraru <
sebastian.muraru at grabtop.upb.ro> wrote:

> Hi there!
>
> I am a Masters student trying to figure things out. I am trying to
> calculate the contact surface area between two molecules. I am aware of the
> classic formula, which is CSA = (SASA(complex) - (SASA(molecule1) +
> SASA(molecule2) ) ) divided by 2 and I am aware that we can make graphs for
> each of these terms using gmx sasa. However, if I want to make a CSA graph
> how do I "jump" from knowing how to make the 3x SASA graphs and combine
> them into one graph?
>
>
You can get the time series of these values easily in their own files and
write a post-processing script to read the values from files and do the
math. You can use any language you like. It's very simple to do in
languages like Python or Perl.

-Justin

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Justin A. Lemkul, Ph.D.

Assistant Professor

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Virginia Tech Department of Biochemistry
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