AMBER Archive (2009)

Subject: Re: [AMBER] hbond analysis

From: Bala subramanian (bala.biophysics_at_gmail.com)
Date: Mon Feb 09 2009 - 12:33:39 CST

Hai Aneesh,

If you want to make the plot of hbond distance Vs time, try carnal. It will
give hbond present in each frame of the trajectory which you can extract. It
is excluded form Amber package now.

Please search amber mail list archive, you will find lots of information on
the interpretaion of hbond analysis using ptraj.

Bala

On Mon, Feb 9, 2009 at 6:55 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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