Hi,
On Sun, Apr 17, 2016 at 12:59 AM, Saman Yousuf ali
<saman.yousufali64.yahoo.com> wrote:
> Dear All,
> I am doing analysis of 5 ns trajectories, which I have run using Amber 14. I have calculated hydrogen bond to track all solute-solute and solute-solvent hydrogen bonds using cpptraj. Now I want to plot the distance between these hydrogen bond vs time.
> SolventAcc THA_533.H13 THA_533.N27 7451 0.2980 2.8909 154.2805
> In above pasted cpptraj hydrogen bond result, solvent is making hydrogen bond with THA (ligand). For running distance command, I will mention 533.N27 for ligand but for solvent Acc I do not know the number. So Kindly tell me how can I able to plot distance vs time for these two ligand and solvent atoms.
This is a hydrogen bond between solute and *any* solvent molecule, so
there is no one specific pair of atoms with which to calculate a
distance. What you could probably do is use the 'closest' command to
keep the closest solvent molecule to :533.N27 and then calculate that
distance.
-Dan
> Thank you.
> Best Regards, Saman Yousuf Ali
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Daniel R. Roe, PhD
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University of Utah
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Received on Mon Apr 18 2016 - 08:00:03 PDT
