Re: [AMBER] Distance calculation using cpptraj

From: Daniel Roe via AMBER <amber.ambermd.org>
Date: Mon, 6 Feb 2023 08:12:18 -0500

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
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