[gmx-users] Hydrogen existence time

aiswarya pawar aiswarya.pawar at gmail.com
Fri Aug 26 11:12:55 CEST 2011


Am trying out the procedure u have mentioned but on the other hand i found
out a article which mentions does the same.


The article states-

use the g_hbond program to analyse hydrogen bonds. First select protein
twice, to get the intramolecular hydrogen bonds, then select protein and
water to get the protein-water h-bonds. Compare the numbers, and their
fluctuations. Is there a trend in the graphs, or a correlation between them?
You can also compute the residence time of the water molecules on the
different functional groups of the protein., e.g. the Ala sidechain. For
this we will have to make an index file first:

% make_ndx -f after_em_sol << EOF
a OW
% g_hbond -contact -n index -ac -r 0.6 -b 200
In the g_hbond command select Sidechain and OW. The -c option computes the
autocorrelation function of the contact time between Cβ and OW. View the
file hbac.xvg using xmgrace. Use xmgrace to integrate the ACF, this will
give you the correlation time. Is it higher or lower than you expected? Why?

Now do the same analysis for interactions between Carbonyl groups and Amide
groups and water oxygens. For these analyses you should put the distance to
0.35, the largest hydrogen bonding distance. Compare the residence times
with that on the hydrophobic sidechain.

as it mentioned the -contact wouldnt include any H bonds between the groups.
but i didnt understand what does OW states cause already there is an option
for water.
does this procedure be good for an residence time.


On Thu, Aug 25, 2011 at 5:18 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 25/08/2011 12:00 AM, aiswarya.pawar at gmail.com wrote:
> Mark,
> The residence time equation goes like this-
> P(r)= function (N(t) - N(t+r))dt
> Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0. N(t) index of water molecule found in the hydration site at time t.
> So that's the autocorrelation of the existence function. Now you need a
> geometric criterion for existence. Note that g_hbond with well-constructed
> groups will calculate the autocorrelation of the existence function for an
> H-bond. See g_hbond -h.
> g_dist, some scripting and g_analyse might be necessary for other criteria.
> Mark
>  Aiswarya
> ------Original Message------
> From: Mark Abraham
> To: Aiswarya Pawar
> Subject: Re: [gmx-users] Hydrogen existence time
> Sent: 24 Aug 2011 6:09 PM
> On 24/08/2011 10:31 PM, aiswarya.pawar at gmail.com wrote:
>  Any idea how can I calculate the residence time of water.
>  First, seek define what you mean to calculate. If you can't write an
> equation down for it, you can't calculate it.
> Mark
> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
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