[AMBER] Distance calculation using cpptraj

From: Dulal Mondal via AMBER <amber.ambermd.org>
Date: Wed, 1 Feb 2023 00:14:30 +0530

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 - 11:00:03 PST
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