[AMBER] Determine whether water molecules are with 1 Å of crystal waters from the PDB structure during the MD simulation

From: Eduard Neu via AMBER <amber.ambermd.org>
Date: Wed, 21 Jun 2023 23:25:47 +0200

Hey guys,

The title basically describes my question. I have a crystal structure of
a protein, and in this structure, there are some crystal waters. I ran a
simulation of this protein and I'm trying to analyze the trajectory.
Basically, I want to determine every frame in which an oxygen atom of a
water molecule is within 1 Å of the original crystal water.

I tried to use CPPTRAJ’s nativecontacts command, but I couldn't figure
out how to measure the distance to a fixed position rather than to an atom.

I came across this paper titled "Diverse GPCRs exhibit conserved water
networks for stabilization and activation." They basically did what I
want to do. In the supporting information, it says:

"To compute the occupancy of water molecules proximal to each
crystallographic water position, we identified amino acid residues
within 5 Å of the crystallographic water's position and aligned all
simulation frames on these residues. We then calculated the fraction of
simulation frames in which a water molecule is within 1 Å of the
crystallographic water position."

But I couldn't really figure out which tool to use for this. Does
anybody have a suggestion?

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Received on Wed Jun 21 2023 - 14:30:01 PDT
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