Determine whether water molecules are with 1 Å of crystal waters from the PDB structure during the M

GROMACS version:2023.1
GROMACS modification: No

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?

I also posted this question in the AMBER Mailing List.