[gmx-users] Binding cavity analysis

Ullmann, Thomas thomas.ullmann at mpibpc.mpg.de
Sun Aug 12 00:57:14 CEST 2018


I forwarded your email to the GROMACS users list,
please use it for user questions. In this way you
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>I have a 2 microsecond trajectory of protein-ligand system. I want to calculate 3 things:
>1. Time series of number of water molecules in binding cavity.

Give gmx select a try. You could select water molecules within
a certain distance of atoms of cavity lining residues.

>2. Volume evolution of in the binding cavity.

There are a number of tools not distributed with GROMACS
that you could try, for example
trj_cavity htt<https://sourceforge.net/projects/trjcavity/>ps://sourceforge.net/projects/trjcavity/<https://sourceforge.net/projects/trjcavity/>
and caver https://www.caver.cz

>3. Water surface density evolution in the cavity.

I'm not sure how you would define this quantity
but a combination of the select and sasa tools of
gmx may work.


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