[AMBER] Can cpptraj hbond command measure second order water bridge ?

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From: xiangyu via AMBER <amber.ambermd.org>
Date: Mon, 1 Jan 2024 19:21:07 +0800 (GMT+08:00)

Hallo ambers,

Can hbond command in cpptraj measure second order water bridge between protein and ligand. A higher order water bridge is defined as more than one water bridging hydrogen bond acceptor and donor. The following command I have tried only gave frequencies for formation of single water bridge(only one molecule between protein ligand)

hbond All1 out All.hbvtime.dat solventdonor :HOH solventacceptor :HOH.O avgout All.UU.avg.dat solvout All.UV.avg.dat bridgeout All.bridge.avg.dat bridgebyatom distance 3.5 angle 110

Thanks
XIang

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Received on Mon Jan 01 2024 - 03:30:02 PST