AMBER Archive (2009)

Subject: [AMBER] hbond analysis

From: aneesh cna (aneeshcna_at_gmail.com)
Date: Mon Feb 09 2009 - 11:55:25 CST

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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