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 <amber.ambermd.org>
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 Ã… 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 Ã… 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 Ã… 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
Bldg. 092/3.92
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Thu Jun 22 2023 - 00:00:02 PDT
