CHARMM Development Project Forums User Discussion & Questions General Chemistry Discussions I have a confusing strange question about the analysis.......

If I want to analyze the continuation time of the hydrogen bond between protein and DNA and try to find when it beyond the range of distance and angle of the hydrogen bond.

What is the physical meaning?
What does the analysis mean?
Are there are references?
Thank you very much.

It seems that you want to analyze the lifetime of hydrogen bonds between protein and DNA. I do not understand how this time could be "beyond the range of distance and angle of the hydrogen bond".

The physical meaning of the (average) lifetime of a particluar hydrogen bond is straightforward; its chemical/biological relevance may be that a long-lived hydrogen bond contributes significantly to the stability of the complex you are looking at. A literature search should give dozens of hits.

Thank you very much.
The meaning is I want to find out the first time the hydrogen bond is absent is when.
What does accentuate on the first time mean?
Thank you very much.

I am sorry, but your messges are really very confusing. I simply have no idea at all what you are talking about.

The meaning is I want to find out the first time the hydrogen bond is absent is when.
What does accentuate on the first time mean?
Thank you very much.

One simple way to find out when a specific hydrogen bond disappears is to plot the hydrogen-acceptor distance vs time.
I don't know what "accentuate on the first time" means. Where did you read this?

My lab ,someone to analyze the distance of hydrogen bond vs the time between the protein and water. And to judge the first time it disappears is when. And to calculate the number of disappeared hydrogen bond and plot the number vs the passed time it disappears.
And this time I want to analyze the hydrogen bond between protein and DNA use the same method .
I want to know the analysis is in what application.
Are there references?
Thank you very much.

Future versions of CHARMM (c32+) will compute H-bond lifetime histograms via COOR HBOND, but for now you'd have tabulate that data yourself from the detailed data produced by the VERBose option. You'd probably have to write a program of some sort to do that.

With the current COOR HBOND (corman.doc) implementation, by using the solute as the first atom selection and water as the second (w/o VERBose), you can get a summary listing of solute H-bond sites and both the average occupancy (frames with H-bond/number of frames analyzed) and the average lifetime. Apply this to the protein alone, DNA alone, and protein:DNA complex, and you get the water part of the story.

(If one assumes that H-bond breaking is a Poisson process with a simple exponential decay, the average is about equal to the std dev, so the average lifetime could be used to estimate the decay.)

For the other part of the story, alternately use the protein and the DNA as the first atom selection, with the other as the second, to get listings of the protein and DNA sites involved in stabilizing the complex.

If you used PBC, it may be necessary to use MERGE COOR RECENTER first (dynamc.doc), so that the H-bond counts won't be lowered by missing molecules when the solute(s) are at the cell boundary. As with lifetime histograms, future versions of COOR HBOND will include provisions to handle PBC directly (for most translation-only shapes).