maybe something like the cpptraj "inmask" would help. you can loop over
atoms in the mask, perhaps setting the mask to be water molecules within a
certain distance of your WT1 residue.
# calculate distance of any N within 10 angstroms of residue 4 atom O
for atoms A0 inmask :4.O
# find nearby N
for atoms A1 inmask .N&\$A0<.10.0
distance \$A0 \$A1 out $F.O-N.dist.\$A0-\$A1.dat
done
done
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 Tue Jan 31 2023 - 12:30:03 PST
