[AMBER] H bonding

From: Dulal Mondal via AMBER <amber.ambermd.org>
Date: Fri, 10 Feb 2023 17:21:29 +0530

Dear Users,

*I have a system (protein in explicit solvent). *
*Protein part: Human carbonic anhydrase II (HCA II), a metallo enzyme.*

*In HCA II, the Zn atom is tetrahedrally coordinated by three histidine
residues and a water molecule. The resname of the Zn coordinated water
molecule is WT1. *

*In HCA II there is another residue Histidine 64. The proton transfer
occurs from Zn coordinated water (WT1) to His-64 via 3 or 4 water
molecules. *

*I am trying to cluster them. If two groups (WT1 and His-64) are in the
same cluster, the proton transfer occurs. *

*My question is how can I cluster them?*

*Water part: TIP3P*

*Thanking You,*

*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Fri Feb 10 2023 - 04:30:02 PST
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