Re: [AMBER] [Sender Not Verified] Determine whether water molecules are with 1 Å of crystal waters from the PDB structure during the MD simulation

From: Eduard Neu via AMBER <>
Date: Tue, 27 Jun 2023 19:07:46 +0200

Hi Thomas,

thank you very much for your informative answer! It worked perfectly.

I moved a chlorine ion to the position of the crystal water with:

translate <mask> topoint x,y,z

Then I checked for the closest distance to water molecules with

nativecontacts <chlorine> <oxygens of solvent> includesolvent name
mindist out mindist.csv

Using a chlorine ion as a ‘probe’ for the distance analysis is a cool
idea and worked perfectly fine.

I’m wondering if it is possible to pick x,y,z coordinated in the mask
for the distance action. So just to use x,y,z coordinates as a ‘probe’.
I couldn’t find any information on that in the cpptraj manual. Would it
be difficult/worthwhile to implement this?


On 6/22/2023 8:42 AM, Steinbrecher, Thomas wrote:
> Hi Eddy,
> this sounds like a hacky solution to me, but you could try to 'move'
> one of your (non-water) atoms in the system to the crystal water
> position you'd like to check with ccptraj's "translate mask topoint x
> y z" command, then use the moved atom as a 'probe' for your distance
> analysis. You'll get a messed up structure if you move say a Calpha
> alone to a random point in space, but as long as you dont do energy
> calculations, the distance analysis should work?
> Kind Regards,
> Thomas
> On Wed, Jun 21, 2023 at 11:26 PM Eduard Neu via AMBER
> <> wrote:
> 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?
> Best
> Eddy
> _______________________________________________
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> --
> *Dr. Thomas Steinbrecher*
> Principal Scientist CADD
> Roche Pharma Research and Early Development
> Roche Innovation Center Basel
> F. Hoffmann-La Roche Ltd
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Received on Tue Jun 27 2023 - 10:30:02 PDT
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