thank youfor your help! i should make my question more clear. i calculated
the H-bond occupied by PTRAJ in AMBER. the cutoff of distance and angle of
hydrogen bond is 3.5 and 120.0, respectively.
i know the mean of "%occuped" between two atoms, for example, the %occupied
between the O6 of ligand and the OD1 of ASP184 is 98.4%. it is presents the
percentual fraction of existence of the hydrogen bond out of the total time
of simultaion is 98.4. but there also exist the hydrogen bond between the O6
and the OD2 of ASP184. so, how can we express the total %occupied of H-bond
between O6 and ASP184?
On 9/16/05, Carlos Simmerling <carlos.simmerling.stonybrook.edu> wrote:
>
> maybe the original question is how to determine the % of time these two
> GROUPS
> are hydrogen bonded, and ptraj gives the % for the specific atom pairs.
>
> For example, if the two atom pairs are H-bonded 50% each, it could be that
> 50% of the time there is a bifurcated Hbond and 50% no Hbond, or
> it could be that It is 1 Hbond in 50% and the other in 50%, so 100%
> of the time there is an Hbond between the groups. There just isn't a way
> to tell that from the average data, you'll need to do some processing of
> the
> Hbonds vs time and see how often you have at least 1 of them.
>
> If this isn't what you meant, please try to clarify exactly what you
> want to calculate.
>
>
> Thomas E. Cheatham, III wrote:
>
> >>I have gotten the hydrogen bond occupied. But in the followed two
> example, I
> >>don't know how to express the %occupied.
> >>
> >>atom
> >>
> >>residue
> >>
> >>distance
> >>
> >>%occupied
> >>
> >>WAT471-O(H1)
> >>
> >>ASP220 (OD2)
> >>
> >>2.697
> >>
> >>55.20
> >>
> >>
> >
> >>From the information given, it is not clear where you obtained the data
> >shown, but if this was the hydrogen bond facility of ptraj, you in the
> >above observed an average distance (when formed, i.e. < cutoff) of 2.697
> >angstroms and an occupancy of 55.2% (meaning that it was formed slightly
> >more than half the time). Occupancies and average distances will depend
> >on the definition of the h-bond (cutoff distance, angle). If the distance
> >cutoff is longer, the occupancy may be higher.
> >
> >
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Received on Mon Sep 19 2005 - 05:53:01 PDT
