AMBER Archive (2009)

Subject: Re: [AMBER] hbond_ptraj

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Wed May 27 2009 - 19:39:15 CDT

> I am trying to calculate the hbond using ptraj
...
> hbond includeself distance 3.6 angle 120 out intra_Hbond.out

add in "series h1"

Also, you may try a larger cutoff than 3A (as per the output below). vdw
radii for N+O ~= 1.66 + 1.908 or ~3.6.

> 1> HBOND
> data will be sorted, intra-residue interactions will be included,
> Distance cutoff is 3.00 angstroms, angle cutoff is 120.00 degrees
                           ^^^^

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