# Re: [AMBER] standard deviation of Hbond lengths and angles

From: Hai Nguyen <nhai.qn.gmail.com>
Date: Mon, 7 Dec 2015 15:24:16 -0500

just want to add to Dan's comment.

If you (Hadeer) know about Python, you can use pytraj (python front end of
cpptraj) to gain more control to cpptraj without update C++ code.
I have a tutorial here relating to hbond with some statistics:
http://amber-md.github.io/pytraj/latest/tutorials/plot_hbond_basic.html

The main idea is similar to Dan's comment
+ use pytraj's hbond to call cpptraj calculation to get a series of makes
+ compute distance and angle for all given makes
+ do the filtering to get only distances and angles that form hbond
+ use numpy to do stat

sounds complicated but all are in above tutorial. (But in the future, both
cpptraj/pytraj will definitely have ready-to-used data)

Hope this help

Hai

On Mon, Dec 7, 2015 at 11:04 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> Hi,
>
> On Sun, Dec 6, 2015 at 8:20 AM, Hadeer ELHabashy
> > Is it possible to calculate the standard deviation of the Hydrogen
> bonding
> > 's lengths and angles directly using the Hbond command ?!
>
> It's certainly possible, but currently not straightforward. This data
> is currently not stored by the 'hbond' command. What you would
> currently have to do is save the hydrogen bond time series data (using
> the "series" keyword), read that data back in, then use a combination
> of the 'filter' command with the 'hbond' series data followed by the
> 'distance'/'angle' commands to calculate the raw distance and angle
> values when the hydrogen bond is present, and lastly calculate your
> average/stdev from those values (using e.g. the 'avg' analysis
> command). The problem is you would have to do this for *each* hydrogen
> bond separately, which is going to be pretty slow.
>
> This is certainly something I can consider adding to cpptraj 'hbond'
> output at some point.
>
> -Dan
>
> PS - If you have any programming experience, it may be easier to e.g.
> modify the HbondType structure in Action_Hbond.cpp to hold the sum of
> squared distances/angles for the purpose of calculating the standard
> deviation yourself.
>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 07 2015 - 12:30:04 PST
Custom Search