Hi,
If all you want is the closest water molecule to residue WT1, you can
use the 'closest' command to select the closest molecule, then
calculate the distance that way.
closest 1 :WT1
distance :WT1.O :WAT.O
-Dan
On Tue, Jan 31, 2023 at 1:45 PM Dulal Mondal via AMBER
<amber.ambermd.org> wrote:
>
> Dear Users,
>
> I have a system (protein in explicit solvent).
>
> Protein part: (Human carbonic anhydrase II), metalloenzyme
>
> It has a Zn ion which is tetrahedrally coordinated by three histidine
> residues and a water molecule.
> The resname of the zn-coordinated water molecule is "WT1".
> Solvent part:
> The resname of solvent water molecules is represented as "WAT".
>
> How can I calculate the distance between the O atom of Zn coordinated water
> (:WT1.O) and a particular solvent molecule of O atom (<mask2>)?
>
> The particular solvent molecule (<mask2>) is defined as follows:
>
> This water molecule forms an H bond with Zn-coordinated water and a
> Threonine-199 residue.
>
> During distance calculation I select the first mask as :WT1.O
>
> "distance :WT1.O <mask2> noimage out distance.dat"
>
> How can I write mask2 in a distance command?
>
> Thanking you
>
>
>
>
> --
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
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Received on Mon Feb 06 2023 - 05:30:03 PST
