Re: [AMBER] Calculation of Intramolecular hydrogen bonding using ptraj

From: Thomas Cheatham III <>
Date: Tue, 27 Jul 2010 09:46:12 -0600 (Mountain Daylight Time)

> I am actually trying to calculate the intramolecular hydrogen bonds that
> exist in a residue in my simulation system. However, I am failing to get any
> output written. I know that intramolecular hydrogen bonds exist in the
> molecule. I have confirmed this by calculating the distances and angles
> using VMD by loading my output file from the simulation.

You can calculate the distances in ptraj too to confirm and/or make sure
that the distances are less than 3.5 angstroms when you visualize. Also,
turn off the angle (angle -1.0); normally I use angle 120.0 which is +/-
60 deg... angle 180 may be assuming it is exactly linear which would be
rare indeed. --tec3

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Received on Tue Jul 27 2010 - 09:00:10 PDT
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