AMBER Archive (2009)

Subject: Re: [AMBER] hbond analysis

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Feb 09 2009 - 12:52:14 CST

I did a google search for ptraj maxocc and found some very helpful results,
especially from Tom Cheatham who wrote ptraj.
http://www.google.com/search?q=ptraj+maxocc
can you take a look at those, and let us know what specific things are still
unclear?
good luck...

On Mon, Feb 9, 2009 at 12:55 PM, aneesh cna <aneeshcna_at_gmail.com> wrote:

> Dear Amber users,
>
> I am using Amber 9.0 for MD simulations. I have some
> doubts with hydrogen bond analysis in ptraj.I did hbond ananlysis for 10ns
> trajectories.Part of hbond output is given below
>
>
> *************************************************************************************************************************************************************************
> Dumping schematic of time series after each h-bond, key follows:
> | . - o x
> * @ |
> 0-5% 5-20% 20-40% 40-60% 60-80% 80-95% 95-100% occupancy
>
> DONOR ACCEPTORH ACCEPTOR
> atom# :res_at_atom atom# :res_at_atom atom# :res_at_atom %occupied
> distance angle lifetime maxocc
> | 8617:6436_at_O1 | 8511 :6430_at_H1 8510 :6430_at_N1 | 77.09 2.803 (
> 0.09) 17.51 ( 8.82) 10.5 ( 13.5) 145 |x**@@x.*****x-**o*x*|
> | 8623:6436_at_O2 | 8468 :6428_at_H2 8466 :6428_at_N1 | 76.69 2.800 (
> 0.09) 17.27 ( 8.90) 11.2 ( 14.6) 149 |o******xo*x-ox**xxo@|
> | 8624:6437_at_O1 | 8137 :6413_at_H1 8136 :6413_at_N1 | 72.21 2.807 (
> 0.09) 19.77 (11.27) 7.3 ( 9.2) 93 |o***o*@**xxo.oxxx**x|
>
> **************************************************************************************************************************************************************************
>
> What is mean by 'lifetime' and 'maxocc' ?
>
> What is mean by the values in parentheses?
>
> How can I interpret ' x**@@x.*****x-**o*x* ' with my 10ns simulation?
>
>
> How will I get a plot of hydrogen bond distance between two atoms as a
> function of time?
>
>
>
> Thanks in advance
> Aneesh
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