Hi,
Both did not match with 3.0 cutoff
I could not fid out the cutoff angle in ptraj, if I use angle as 90 I get more hybond than when I use 180,
What it signifies
Mannan
--- On Fri, 3/9/10, Daniel Roe <daniel.r.roe.gmail.com> wrote:
From: Daniel Roe <daniel.r.roe.gmail.com>
Subject: Re: [AMBER] Hbond Analysis
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Friday, 3 September, 2010, 5:25 PM
Hi,
On Fri, Sep 3, 2010 at 5:03 AM, Mannan <malie_03.yahoo.co.in> wrote:
> I am using ptraj hbond to calculate the % of hydrogen bond occurrence in the trajectory.
> hough I could see the many Hbonds in VMD, but the results from hbond ptraj could show only two hbond.
> The Hbond analysis shows only few.
> hbond print .05 series hbt
The results from the hbond command in ptraj are of course sensitive to
the distance/angle cutoffs you choose. The default distance cutoff for
VMD is 3.0 Ang, while the default distance cutoff in ptraj is 3.5 (see
section 6.9 in the AmberTools manual for more details). Try running:
hbond distance 3.0 print .05 series hbt
And see if that brings the results more in-line with each other.
-Dan
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Received on Fri Sep 03 2010 - 05:30:05 PDT
