Hi Eddy,
Im just speculating here, but I doubt this is possible or likely to be
implemented. There is always the assumption that absolute coordinates are
meaningless and only relative ones are of interest, so the translate to
point command is in itself a bit of an outlier in Amber. Otoh, vmd accepts
'x>5' type absolute coordinate selections and maybe doing analysis or
preprocessing there could be an alternative if you definitely need to
select by cartesian coordinates.
Kind Regards,
Thomas
On Tue, Jun 27, 2023 at 7:07 PM Eduard Neu <eduard.neu.fau.de> wrote:
> 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:
>
> 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?
>
> Best
> Eddy
>
> 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 <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
>
>
--
*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 Tue Jun 27 2023 - 23:30:03 PDT
