AMBER Archive (2009)

Subject: Re: [AMBER] Variations of the number of total hydrogen bond in MD simulations using ptraj

From: Paul Frybarger (paul.frybarger_at_hope.edu)
Date: Mon Aug 17 2009 - 12:57:28 CDT

Hello,

It would appear that this is a case where RTFS trumps RTFM. There is an
option to set the print level in ptraj which appears not to be documented.
If you set 'prnlev' to a value greater than 1 then the raw hbond data will
be dumped for each frame. It should look like

trajin foo
prnlev 2

hbond foo...

It will dump each hbond it finds in a format like:

HBOND 14: 1 O -- 3780:1226 H2 3778:1226 O 2.68 angstroms,
163.62 degrees

It might take some effort to parse the output and find the number of bonds,
but it should be doable. Good luck!

- Paul Frybarger

On Mon, Aug 17, 2009 at 6:26 AM, workalemahu berhanu <wgberhanu_at_gmail.com>wrote:

> Dear Dr Ross
> Hi
> If you remember I asked you this same question at the summer workshop
> at UCSD. Your advice was to post my question on the forum. May be the
> way I put my question was not so clear. I have attached a graph that
> shows the change in the number of total hydrogen bonds versus the
> simulation time. I am interested in getting the raw data to make
> similar plot from my trajectory file
>
> With regards
>
> Thank you
>
>
> On Sun, Aug 16, 2009 at 8:30 PM, Ross Walker<ross_at_rosswalker.co.uk> wrote:
> > See section 6 of tutorial B3 :
> > http://ambermd.org/tutorials/basic/tutorial3/section6.htm
> >
> > It should be fairly easy for you to modify the donor / acceptor
> definitions
> > for your system.
> >
> > Good luck,
> > Ross
> >
> >> -----Original Message-----
> >> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> >> Behalf Of workalemahu berhanu
> >> Sent: Sunday, August 16, 2009 1:13 PM
> >> To: AMBER Mailing List
> >> Subject: [AMBER] Variations of the number of total hydrogen bond in MD
> >> simulations using ptraj
> >>
> >> Dear amber users
> >> I would like to analysis my trajectory file for the change in the
> >> total number of hydrogen bonds in my peptide and peptide with ligand
> >> which is having beta sheet secondary structure in MD simulation. Is it
> >> possible to do it using ptraj? Could anyone provide me a script for
> >> this kind of analysis?
> >> Thank you
> >> With regards
> >>
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> >
> >
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